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Sample records for affine registration method

  1. Bidirectional Elastic Image Registration Using B-Spline Affine Transformation

    PubMed Central

    Gu, Suicheng; Meng, Xin; Sciurba, Frank C.; Wang, Chen; Kaminski, Naftali; Pu, Jiantao

    2014-01-01

    A registration scheme termed as B-spline affine transformation (BSAT) is presented in this study to elastically align two images. We define an affine transformation instead of the traditional translation at each control point. Mathematically, BSAT is a generalized form of the affine transformation and the traditional B-Spline transformation (BST). In order to improve the performance of the iterative closest point (ICP) method in registering two homologous shapes but with large deformation, a bi-directional instead of the traditional unidirectional objective / cost function is proposed. In implementation, the objective function is formulated as a sparse linear equation problem, and a sub-division strategy is used to achieve a reasonable efficiency in registration. The performance of the developed scheme was assessed using both two-dimensional (2D) synthesized dataset and three-dimensional (3D) volumetric computed tomography (CT) data. Our experiments showed that the proposed B-spline affine model could obtain reasonable registration accuracy. PMID:24530210

  2. Bidirectional elastic image registration using B-spline affine transformation.

    PubMed

    Gu, Suicheng; Meng, Xin; Sciurba, Frank C; Ma, Hongxia; Leader, Joseph; Kaminski, Naftali; Gur, David; Pu, Jiantao

    2014-06-01

    A registration scheme termed as B-spline affine transformation (BSAT) is presented in this study to elastically align two images. We define an affine transformation instead of the traditional translation at each control point. Mathematically, BSAT is a generalized form of the affine transformation and the traditional B-spline transformation (BST). In order to improve the performance of the iterative closest point (ICP) method in registering two homologous shapes but with large deformation, a bidirectional instead of the traditional unidirectional objective/cost function is proposed. In implementation, the objective function is formulated as a sparse linear equation problem, and a sub-division strategy is used to achieve a reasonable efficiency in registration. The performance of the developed scheme was assessed using both two-dimensional (2D) synthesized dataset and three-dimensional (3D) volumetric computed tomography (CT) data. Our experiments showed that the proposed B-spline affine model could obtain reasonable registration accuracy. PMID:24530210

  3. Virtual-real spatial information visualization registration using affine representations

    NASA Astrophysics Data System (ADS)

    Wu, Xueling; Ren, Fu; Du, Qingyun

    2009-10-01

    Virtual-real registration in Outdoor Augmented Reality is committed to enhance user's spatial cognition by overlaying virtual geographical objects on real scene. According to analyze fiducial detection registration method in indoor AR, for the purpose of avoiding complex and tedious process of position tracking and camera calibration in traditional registration methods, it puts forward and practices a virtual-real spatial information visualization registration method using affine representations. Based on the observation from Koenderink and van Doorn, Ullman and Basri in 1991 which is given a set of four or more non-coplanar 3D points, the projection of all points in the set can be computed as a linear combination of the projection of just four of the points, it sets up global affine coordinate system in light of world coordinates, camera coordinates and virtual coordinates and extracts four feature points from scene image and calculates the global affine coordinates of key points of virtual objects. Then according to a linear homogeneous coordinates of the four feature point's projection, it calculates projection pixel coordinates of key points of virtual objects. In addition, it proposes an approach to obtain pixel relative depth for hidden surface removal. Finally, by a case study, it verifies the feasibility and efficiency of the registration methods. The method would not only explore a new research direction for Geographical Information Science, but also would provide location-based information and services for outdoor AR.

  4. 3D affine registration using teaching-learning based optimization

    NASA Astrophysics Data System (ADS)

    Jani, Ashish; Savsani, Vimal; Pandya, Abhijit

    2013-09-01

    3D image registration is an emerging research field in the study of computer vision. In this paper, two effective global optimization methods are considered for the 3D registration of point clouds. Experiments were conducted by applying each algorithm and their performance was evaluated with respect to rigidity, similarity and affine transformations. Comparison of algorithms and its effectiveness was tested for the average performance to find the global solution for minimizing the error in the terms of distance between the model cloud and the data cloud. The parameters for the transformation matrix were considered as the design variables. Further comparisons of the considered methods were done for the computational effort, computational time and the convergence of the algorithm. The results reveal that the use of TLBO was outstanding for image processing application involving 3D registration. [Figure not available: see fulltext.

  5. Affine and deformable registration based on polynomial expansion.

    PubMed

    Farnebäck, Gunnar; Westin, Carl-Fredrik

    2006-01-01

    This paper presents a registration framework based on the polynomial expansion transform. The idea of polynomial expansion is that the image is locally approximated by polynomials at each pixel. Starting with observations of how the coefficients of ideal linear and quadratic polynomials change under translation and affine transformation, algorithms are developed to estimate translation and compute affine and deformable registration between a fixed and a moving image, from the polynomial expansion coefficients. All algorithms can be used for signals of any dimensionality. The algorithms are evaluated on medical data. PMID:17354971

  6. Automatic registration of multisensor images with affine deformation based on triangle area representation

    NASA Astrophysics Data System (ADS)

    Li, Bin; Wang, Wei; Ye, Hao

    2013-01-01

    A new automatic feature-based registration algorithm of multisensor images with affine deformation is presented. Although the feature-based registration methods have an advantage in reducing computational load over the area-based ones, certain typical issues such as complex deformation and grayscale discrepancy existing in a multisensor image pair will make the design of a robust feature descriptor challenging. To deal with these issues, in contrast with most existing feature-based methods that describe feature points directly, we introduce an additional procedure of feature quadrilateral construction in the proposed algorithm. Then the descriptors for the constructed feature quadrilaterals are designed based on the affine-invariance property of triangle area representation. By doing these, the proposed algorithm's robustness to both affine deformation and grayscale discrepancy can be guaranteed. Besides, since the calculation of feature descriptors only involves simple algebraic operations, the proposed method has low computational load. Experimental results using real multisensor image pairs are presented to show the merits of the proposed method.

  7. Registration algorithm research for work-pieces based on affine invariant

    NASA Astrophysics Data System (ADS)

    Chen, Meng; Yan, Bixi

    2011-11-01

    Work-pieces registration is a crucial item in flexible manufacture assembly. In order to finish work-pieces registration, a method is proposed based on affine invariant. After the CAD model data and actual measurement data of a work-piece are acquired, the method consists of the following five steps: sampling point clouds data, extracting characteristic four-points set, searching characteristic congruent four-points set, computing transformation congruent matrix and the last, further precise point clouds data registration. Point clouds data of CAD and measuring model are sampled respectively through calculating the curvature of the two sets of data and selecting the obvious curvature points as their reduced characteristic points. Based on this, the characteristic four-points set from the reduced ones of CAD model and the corresponding matching congruent four-points set of the measuring model are extracted according to RANSAC algorithm. The rotation matrix R and translation vector T of any two matching four-points are then calculated through the algorithm of quaternion. After that, the measuring model is rotated and translated and then compared with the CAD model data, the most congruent transformation matrix is selected as the coarse registration result. Furthermore, Iterative Closest Point (ICP) algorithm is applied to the congruent transformation to improve registration precision. The experiment shows that the run time of the algorithm is 129.56s and mean-error of point-to-point distance is 0.062mm when accessing measuring model data more than 80000 points. Compared with the traditional curvature registration, the experiment also shows that the algorithm is more efficient and robust when the volume of point clouds data is larger.

  8. Speckle reduction in optical coherence tomography imaging by affine-motion image registration

    NASA Astrophysics Data System (ADS)

    Alonso-Caneiro, David; Read, Scott A.; Collins, Michael J.

    2011-11-01

    Signal-degrading speckle is one factor that can reduce the quality of optical coherence tomography images. We demonstrate the use of a hierarchical model-based motion estimation processing scheme based on an affine-motion model to reduce speckle in optical coherence tomography imaging, by image registration and the averaging of multiple B-scans. The proposed technique is evaluated against other methods available in the literature. The results from a set of retinal images show the benefit of the proposed technique, which provides an improvement in signal-to-noise ratio of the square root of the number of averaged images, leading to clearer visual information in the averaged image. The benefits of the proposed technique are also explored in the case of ocular anterior segment imaging.

  9. Combining local affine frames and SIFT for remote sensing image registration

    NASA Astrophysics Data System (ADS)

    Sun, Hao; Wang, Cheng; Hao, Shengyong

    2009-10-01

    Local invariant features such as scale invariant feature transform (SIFT) have received considerable attention in recent years. Despite its tremendous success in computer vision applications, SIFT matching alone is not sufficient for remote sensing image registration because of low detection repeatablility and nonlinear intensity changes. In this paper, we introduce a remote sensing image registration algorithm that combines local affine frames (LAF) together with SIFT matching. Firstly, distinctive SIFT keypoints and maximally stable extremal regions (MSER) are detected independently in the reference image and the sensed image. Contrast reversal invariant SIFT descriptor is constructed for describing texture patches around SIFT keypoints and shape descriptor defined in LAF is constructed for describing MSER contour. Nearest neighbor distance ratio matching with confidence measurement is then adopted to match both descriptors. Tentative correspondences are ranked according to their confidence measurements. Finally, random sample consensus (RANSAC) is performed in the top ranked matched features to obtain a global set of transform parameters. Experimental results demonstrate the robustness and accuracy of the proposed method.

  10. A multicore based parallel image registration method.

    PubMed

    Yang, Lin; Gong, Leiguang; Zhang, Hong; Nosher, John L; Foran, David J

    2009-01-01

    Image registration is a crucial step for many image-assisted clinical applications such as surgery planning and treatment evaluation. In this paper we proposed a landmark based nonlinear image registration algorithm for matching 2D image pairs. The algorithm was shown to be effective and robust under conditions of large deformations. In landmark based registration, the most important step is establishing the correspondence among the selected landmark points. This usually requires an extensive search which is often computationally expensive. We introduced a nonregular data partition algorithm using the K-means clustering algorithm to group the landmarks based on the number of available processing cores. The step optimizes the memory usage and data transfer. We have tested our method using IBM Cell Broadband Engine (Cell/B.E.) platform. PMID:19964921

  11. Comparison of time-series registration methods in breast dynamic infrared imaging

    NASA Astrophysics Data System (ADS)

    Riyahi-Alam, S.; Agostini, V.; Molinari, F.; Knaflitz, M.

    2015-03-01

    Automated motion reduction in dynamic infrared imaging is on demand in clinical applications, since movement disarranges time-temperature series of each pixel, thus originating thermal artifacts that might bias the clinical decision. All previously proposed registration methods are feature based algorithms requiring manual intervention. The aim of this work is to optimize the registration strategy specifically for Breast Dynamic Infrared Imaging and to make it user-independent. We implemented and evaluated 3 different 3D time-series registration methods: 1. Linear affine, 2. Non-linear Bspline, 3. Demons applied to 12 datasets of healthy breast thermal images. The results are evaluated through normalized mutual information with average values of 0.70 ±0.03, 0.74 ±0.03 and 0.81 ±0.09 (out of 1) for Affine, Bspline and Demons registration, respectively, as well as breast boundary overlap and Jacobian determinant of the deformation field. The statistical analysis of the results showed that symmetric diffeomorphic Demons' registration method outperforms also with the best breast alignment and non-negative Jacobian values which guarantee image similarity and anatomical consistency of the transformation, due to homologous forces enforcing the pixel geometric disparities to be shortened on all the frames. We propose Demons' registration as an effective technique for time-series dynamic infrared registration, to stabilize the local temperature oscillation.

  12. Image registration method for medical image sequences

    DOEpatents

    Gee, Timothy F.; Goddard, James S.

    2013-03-26

    Image registration of low contrast image sequences is provided. In one aspect, a desired region of an image is automatically segmented and only the desired region is registered. Active contours and adaptive thresholding of intensity or edge information may be used to segment the desired regions. A transform function is defined to register the segmented region, and sub-pixel information may be determined using one or more interpolation methods.

  13. A non-rigid registration method for mouse whole body skeleton registration

    NASA Astrophysics Data System (ADS)

    Xiao, Di; Zahra, David; Bourgeat, Pierrick; Berghofer, Paula; Acosta Tamayo, Oscar; Wimberley, Catriona; Gregoire, Marie Claude; Salvado, Olivier

    2010-03-01

    Micro-CT/PET imaging scanner provides a powerful tool to study tumor in small rodents in response to therapy. Accurate image registration is a necessary step to quantify the characteristics of images acquired in longitudinal studies. Small animal registration is challenging because of the very deformable body of the animal often resulting in different postures despite physical restraints. In this paper, we propose a non-rigid registration approach for the automatic registration of mouse whole body skeletons, which is based on our improved 3D shape context non-rigid registration method. The whole body skeleton registration approach has been tested on 21 pairs of mouse CT images with variations of individuals and time-instances. The experimental results demonstrated the stability and accuracy of the proposed method for automatic mouse whole body skeleton registration.

  14. Digital image registration method using boundary maps

    NASA Technical Reports Server (NTRS)

    Andrus, J. F.; Campbell, C. W.; Jayroe, R. R.

    1975-01-01

    A new method of automatic image registration (matching) is presented. It requires that the original single or multichannel images first be converted to binary boundary maps having elements equal to zero or unity. The method corrects for both translational and rotational errors. One feature of the technique is the rapid calculation of a pseudo correlation matrix NCOR using only integer additions. It is argued that the use of boundary maps is advisable when the data from the two images are acquired under different conditions; i.e., weather conditions, lighting conditions, etc.

  15. Methods for Improving Aptamer Binding Affinity.

    PubMed

    Hasegawa, Hijiri; Savory, Nasa; Abe, Koichi; Ikebukuro, Kazunori

    2016-01-01

    Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of aptamers. In particular, sequence optimization using combined in silico sequence recombinations and in vitro functional evaluations is effective for the improvement of binding affinities, however, the binding affinities of aptamers are limited by the low hydrophobicity of nucleic acids. Accordingly, introduction of hydrophobic moieties into aptamers expands the diversity of interactions between aptamers and targets. Moreover, construction of multivalent aptamers by connecting aptamers that recognize distinct epitopes is an attractive approach to substantial increases in binding affinity. In addition, binding affinities can be tuned by optimizing the scaffolds of multivalent constructs. In this review, we summarize the various techniques for improving the binding affinities of aptamers. PMID:27043498

  16. Characterization of endothelial function in the brachial artery via affine registration of ultrasonographic image sequences

    NASA Astrophysics Data System (ADS)

    Lamata, Pablo; Laclaustra, Martin; Frangi, Alejandro F.

    2003-05-01

    The assessment and characterization of the endothelial function is a current research topic as it may play an important role in the diagnosis of cardiovascular diseases. Flow mediated dilatation may be used to investigate endothelial function, and B-mode ultrasonography is a cheap and non-invasive way to assess the vasodilation response. Computerized analysis techniques are very desirable to give higher accuracy and objectivity to the measurements. A new method is presented that solves some limitations of existing methods, which in general depend on accurate edge detection of the arterial wall. This method is based on a global image analysis strategy. The arterial vasodilation between two frames is modeled by a superposition of a rigid motion model and a stretching perpendicular to the artery. Both transformation models are recovered using an image registration algorithm based on normalized mutual information and a multi-resolution search framework. Temporal continuity of in the variation of the registration parameters is enforced with a Kalman filter, since the dilation process is known to be a gradual and continuous physiological phenomenon. The proposed method presents a negligible bias when compared with manual assessment. It also eliminates artifacts introduced by patient and probe motion, thus improving the accuracy of the measurements. Finally, it is also robust to typical problems of ultrasound, like speckle noise and poor image quality.

  17. Comparison of demons deformable registration-based methods for texture analysis of serial thoracic CT scans

    NASA Astrophysics Data System (ADS)

    Cunliffe, Alexandra R.; Al-Hallaq, Hania A.; Fei, Xianhan M.; Tuohy, Rachel E.; Armato, Samuel G.

    2013-02-01

    To determine how 19 image texture features may be altered by three image registration methods, "normal" baseline and follow-up computed tomography (CT) scans from 27 patients were analyzed. Nineteen texture feature values were calculated in over 1,000 32x32-pixel regions of interest (ROIs) randomly placed in each baseline scan. All three methods used demons registration to map baseline scan ROIs to anatomically matched locations in the corresponding transformed follow-up scan. For the first method, the follow-up scan transformation was subsampled to achieve a voxel size identical to that of the baseline scan. For the second method, the follow-up scan was transformed through affine registration to achieve global alignment with the baseline scan. For the third method, the follow-up scan was directly deformed to the baseline scan using demons deformable registration. Feature values in matched ROIs were compared using Bland- Altman 95% limits of agreement. For each feature, the range spanned by the 95% limits was normalized to the mean feature value to obtain the normalized range of agreement, nRoA. Wilcoxon signed-rank tests were used to compare nRoA values across features for the three methods. Significance for individual tests was adjusted using the Bonferroni method. nRoA was significantly smaller for affine-registered scans than for the resampled scans (p=0.003), indicating lower feature value variability between baseline and follow-up scan ROIs using this method. For both of these methods, however, nRoA was significantly higher than when feature values were calculated directly on demons-deformed followup scans (p<0.001). Across features and methods, nRoA values remained below 26%.

  18. An improved 3D shape context registration method for non-rigid surface registration

    NASA Astrophysics Data System (ADS)

    Xiao, Di; Zahra, David; Bourgeat, Pierrick; Berghofer, Paula; Acosta Tamayo, Oscar; Wimberley, Catriona; Gregoire, Marie-Claude; Salvado, Olivier

    2010-03-01

    3D shape context is a method to define matching points between similar shapes as a pre-processing step to non-rigid registration. The main limitation of the approach is point mismatching, which includes long geodesic distance mismatch and neighbors crossing mismatch. In this paper, we propose a topological structure verification method to correct the long geodesic distance mismatch and a correspondence field smoothing method to correct the neighbors crossing mismatch. A robust 3D shape context model is proposed and further combined with thin-plate spline model for non-rigid surface registration. The method was tested on phantoms and rat hind limb skeletons from micro CT images. The results from experiments on mouse hind limb skeletons indicate that the approach is robust.

  19. Tools and Methods for the Registration and Fusion of Remotely Sensed Data

    NASA Technical Reports Server (NTRS)

    Goshtasby, Arthur Ardeshir; LeMoigne, Jacqueline

    2010-01-01

    Tools and methods for image registration were reviewed. Methods for the registration of remotely sensed data at NASA were discussed. Image fusion techniques were reviewed. Challenges in registration of remotely sensed data were discussed. Examples of image registration and image fusion were given.

  20. Accurate Evaluation Method of Molecular Binding Affinity from Fluctuation Frequency

    NASA Astrophysics Data System (ADS)

    Hoshino, Tyuji; Iwamoto, Koji; Ode, Hirotaka; Ohdomari, Iwao

    2008-05-01

    Exact estimation of the molecular binding affinity is significantly important for drug discovery. The energy calculation is a direct method to compute the strength of the interaction between two molecules. This energetic approach is, however, not accurate enough to evaluate a slight difference in binding affinity when distinguishing a prospective substance from dozens of candidates for medicine. Hence more accurate estimation of drug efficacy in a computer is currently demanded. Previously we proposed a concept of estimating molecular binding affinity, focusing on the fluctuation at an interface between two molecules. The aim of this paper is to demonstrate the compatibility between the proposed computational technique and experimental measurements, through several examples for computer simulations of an association of human immunodeficiency virus type-1 (HIV-1) protease and its inhibitor (an example for a drug-enzyme binding), a complexation of an antigen and its antibody (an example for a protein-protein binding), and a combination of estrogen receptor and its ligand chemicals (an example for a ligand-receptor binding). The proposed affinity estimation has proven to be a promising technique in the advanced stage of the discovery and the design of drugs.

  1. A new method of synthesizing biopolymeric affinity ligands.

    PubMed

    Chaga, G S; Guzman, R; Porath, J O

    1997-08-01

    (1) A new concept for producing soluble polymeric affinity ligands is proposed and exemplified. By solid-phase synthesis, an insoluble hydrophilic polymer is converted into an affinity gel. The gel is hydrolytically degraded to water-soluble affinity polymeric ligands which are recovered and purified. (2) A water-soluble biopolymeric metal-affinity carrier based on an iminodiacetic acid (IDA) derivative of dextran has been synthesized through the modification of Sephadex G-200 by IDA, followed by hydrolysis with dextranase and size-exclusion-chromatographic purification of the high-molecular-mass fragments. (3) The molecular size of the soluble products as a function of hydrolysis time with dextranase from Penicillium sp. was determined. The range of molecular size of the biopolymeric chelating ligand varies from around 200 Da to greater than 580 kDa. (4) The influence of three metal ions chelated with the Sephadex derivative on the hydrolysis rate and the molecular-size distribution of end products was studied. Eu3+ was found to improve the rate of solubilization. Ni2+ and Cu2+ decreased the hydrolysis rate, as compared with that of the metal-free IDA-Sephadex. (5) The method introduced here has the potential of being developed and applied as a general technology for synthesis of soluble multifunctional affinity ligands. Such ligands should be useful for liquid-phase extraction as well as for the synthesis of adsorbents with localized multiple binding sites. Other possible fields of applications are to be found in medicine, where they could be used for slow drug delivery or detoxification, and in analytical chemistry, where they could be used in various assays. PMID:9261997

  2. Gauss-Newton method for DEM co-registration

    NASA Astrophysics Data System (ADS)

    Wang, Kunlun; Zhang, Tonggang

    2015-12-01

    Digital elevation model (DEM) co-registration is one of the hottest research problems, and it is the critical technology for multi-temporal DEM analysis, which has wide potential application in many fields, such as geological hazards. Currently, the least-squares principle is used in most DEM co-registration methods, in which the matching parameters are obtained by iteration; the surface co-registration is then accomplished. To improve the iterative convergence rate, a Gauss-Newton method for DEM co-registration (G-N) is proposed in this paper. A gradient formula based on a gridded discrete surface is derived in theory, and then the difficulty of applying the Gauss-Newton method to DEM matching is solved. With the G-N algorithm, the surfaces approach each other along the maximal gradient direction, and therefore the iterative convergence and the performance efficiency of the new method can be enhanced greatly. According to experimental results based on the simulated datasets, the average convergence rates of rotation and translation parameters of the G-N algorithm are increased by 40 and 15% compared to those of the ICP algorithm, respectively. The performance efficiency of the G-N algorithm is 74.9% better.

  3. Validation of non-rigid point-set registration methods using a porcine bladder pelvic phantom

    NASA Astrophysics Data System (ADS)

    Zakariaee, Roja; Hamarneh, Ghassan; Brown, Colin J.; Spadinger, Ingrid

    2016-01-01

    The problem of accurate dose accumulation in fractionated radiotherapy treatment for highly deformable organs, such as bladder, has garnered increasing interest over the past few years. However, more research is required in order to find a robust and efficient solution and to increase the accuracy over the current methods. The purpose of this study was to evaluate the feasibility and accuracy of utilizing non-rigid (affine or deformable) point-set registration in accumulating dose in bladder of different sizes and shapes. A pelvic phantom was built to house an ex vivo porcine bladder with fiducial landmarks adhered onto its surface. Four different volume fillings of the bladder were used (90, 180, 360 and 480 cc). The performance of MATLAB implementations of five different methods were compared, in aligning the bladder contour point-sets. The approaches evaluated were coherent point drift (CPD), gaussian mixture model, shape context, thin-plate spline robust point matching (TPS-RPM) and finite iterative closest point (ICP-finite). The evaluation metrics included registration runtime, target registration error (TRE), root-mean-square error (RMS) and Hausdorff distance (HD). The reference (source) dataset was alternated through all four points-sets, in order to study the effect of reference volume on the registration outcomes. While all deformable algorithms provided reasonable registration results, CPD provided the best TRE values (6.4 mm), and TPS-RPM yielded the best mean RMS and HD values (1.4 and 6.8 mm, respectively). ICP-finite was the fastest technique and TPS-RPM, the slowest.

  4. Validation of non-rigid point-set registration methods using a porcine bladder pelvic phantom.

    PubMed

    Zakariaee, Roja; Hamarneh, Ghassan; Brown, Colin J; Spadinger, Ingrid

    2016-01-21

    The problem of accurate dose accumulation in fractionated radiotherapy treatment for highly deformable organs, such as bladder, has garnered increasing interest over the past few years. However, more research is required in order to find a robust and efficient solution and to increase the accuracy over the current methods. The purpose of this study was to evaluate the feasibility and accuracy of utilizing non-rigid (affine or deformable) point-set registration in accumulating dose in bladder of different sizes and shapes. A pelvic phantom was built to house an ex vivo porcine bladder with fiducial landmarks adhered onto its surface. Four different volume fillings of the bladder were used (90, 180, 360 and 480 cc). The performance of MATLAB implementations of five different methods were compared, in aligning the bladder contour point-sets. The approaches evaluated were coherent point drift (CPD), gaussian mixture model, shape context, thin-plate spline robust point matching (TPS-RPM) and finite iterative closest point (ICP-finite). The evaluation metrics included registration runtime, target registration error (TRE), root-mean-square error (RMS) and Hausdorff distance (HD). The reference (source) dataset was alternated through all four points-sets, in order to study the effect of reference volume on the registration outcomes. While all deformable algorithms provided reasonable registration results, CPD provided the best TRE values (6.4 mm), and TPS-RPM yielded the best mean RMS and HD values (1.4 and 6.8 mm, respectively). ICP-finite was the fastest technique and TPS-RPM, the slowest. PMID:26740511

  5. Fourier method for large scale surface modeling and registration.

    PubMed

    Shen, Li; Kim, Sungeun; Saykin, Andrew J

    2009-06-01

    Spherical harmonic (SPHARM) description is a powerful Fourier shape modeling method for processing arbitrarily shaped but simply connected 3D objects. As a highly promising method, SPHARM has been widely used in several domains including medical imaging. However, its primary use has been focused on modeling small or moderately-sized surfaces that are relatively smooth, due to challenges related to its applicability, robustness and scalability. This paper presents an enhanced SPHARM framework that addresses these issues and show that the use of SPHARM can expand into broader areas. In particular, we present a simple and efficient Fourier expansion method on the sphere that enables large scale modeling, and propose a new SPHARM registration method that aims to preserve the important homological properties between 3D models. Although SPHARM is a global descriptor, our experimental results show that the proposed SPHARM framework can accurately describe complicated graphics models and highly convoluted 3D surfaces and the proposed registration method allows for effective alignment and registration of these 3D models for further processing or analysis. These methods greatly enable the potential of applying SPHARM to broader areas such as computer graphics, medical imaging, CAD/CAM, bioinformatics, and other related geometric modeling and processing fields. PMID:20161536

  6. An accurate 3D shape context based non-rigid registration method for mouse whole-body skeleton registration

    NASA Astrophysics Data System (ADS)

    Xiao, Di; Zahra, David; Bourgeat, Pierrick; Berghofer, Paula; Acosta Tamayo, Oscar; Wimberley, Catriona; Gregoire, Marie C.; Salvado, Olivier

    2011-03-01

    Small animal image registration is challenging because of its joint structure, and posture and position difference in each acquisition without a standard scan protocol. In this paper, we face the issue of mouse whole-body skeleton registration from CT images. A novel method is developed for analyzing mouse hind-limb and fore-limb postures based on geodesic path descriptor and then registering the major skeletons and fore limb skeletons initially by thin-plate spline (TPS) transform based on the obtained geodesic paths and their enhanced correspondence fields. A target landmark correction method is proposed for improving the registration accuracy of the improved 3D shape context non-rigid registration method we previously proposed. A novel non-rigid registration framework, combining the skeleton posture analysis, geodesic path based initial alignment and 3D shape context model, is proposed for mouse whole-body skeleton registration. The performance of the proposed methods and framework was tested on 12 pairs of mouse whole-body skeletons. The experimental results demonstrated the flexibility, stability and accuracy of the proposed framework for automatic mouse whole body skeleton registration.

  7. Robust activation method for negative electron affinity photocathodes

    DOEpatents

    Mulhollan, Gregory A.; Bierman, John C.

    2011-09-13

    A method by which photocathodes(201), single crystal, amorphous, or otherwise ordered, can be surface modified to a robust state of lowered and in best cases negative, electron affinity has been discovered. Conventional methods employ the use of Cs(203) and an oxidizing agent(207), typically carried by diatomic oxygen or by more complex molecules, for example nitrogen trifluoride, to achieve a lowered electron affinity(404). In the improved activation method, a second alkali, other than Cs(205), is introduced onto the surface during the activation process, either by co-deposition, yo-yo, or sporadic or intermittent application. Best effect for GaAs photocathodes has been found through the use of Li(402) as the second alkali, though nearly the same effect can be found by employing Na(406). Suitable photocathodes are those which are grown, cut from boules, implanted, rolled, deposited or otherwise fabricated in a fashion and shape desired for test or manufacture independently supported or atop a support structure or within a framework or otherwise affixed or suspended in the place and position required for use.

  8. A novel parametric method for non-rigid image registration.

    PubMed

    Cuzol, Anne; Hellier, Pierre; Mémin, Etienne

    2005-01-01

    This paper presents a novel non-rigid registration method. The main contribution of the method is the modeling of the vorticity (respectively divergence) of the deformation field using vortex (respectively sink and source) particles. Two parameters are associated with a particle: the vorticity (or divergence) strength and the influence domain. This leads to a very compact representation of vorticity and divergence fields. In addition, the optimal position of these particles is determined using a mean shift process. 2D experiments of this method are presented and demonstrate its ability to recover evolving phenomena (MS lesions) so as to register images from 20 patients. PMID:17354717

  9. Robust image registration using adaptive coherent point drift method

    NASA Astrophysics Data System (ADS)

    Yang, Lijuan; Tian, Zheng; Zhao, Wei; Wen, Jinhuan; Yan, Weidong

    2016-04-01

    Coherent point drift (CPD) method is a powerful registration tool under the framework of the Gaussian mixture model (GMM). However, the global spatial structure of point sets is considered only without other forms of additional attribute information. The equivalent simplification of mixing parameters and the manual setting of the weight parameter in GMM make the CPD method less robust to outlier and have less flexibility. An adaptive CPD method is proposed to automatically determine the mixing parameters by embedding the local attribute information of features into the construction of GMM. In addition, the weight parameter is treated as an unknown parameter and automatically determined in the expectation-maximization algorithm. In image registration applications, the block-divided salient image disk extraction method is designed to detect sparse salient image features and local self-similarity is used as attribute information to describe the local neighborhood structure of each feature. The experimental results on optical images and remote sensing images show that the proposed method can significantly improve the matching performance.

  10. A method for quantitative analysis of regional lung ventilation using deformable image registration of CT and hybrid hyperpolarized gas/1H MRI.

    PubMed

    Tahir, Bilal A; Swift, Andrew J; Marshall, Helen; Parra-Robles, Juan; Hatton, Matthew Q; Hartley, Ruth; Kay, Richard; Brightling, Christopher E; Vos, Wim; Wild, Jim M; Ireland, Rob H

    2014-12-01

    Hyperpolarized gas magnetic resonance imaging (MRI) generates highly detailed maps of lung ventilation and physiological function while CT provides corresponding anatomical and structural information. Fusion of such complementary images enables quantitative analysis of pulmonary structure-function. However, direct image registration of hyperpolarized gas MRI to CT is problematic, particularly in lungs whose boundaries are difficult to delineate due to ventilation heterogeneity. This study presents a novel indirect method of registering hyperpolarized gas MRI to CT utilizing (1)H-structural MR images that are acquired in the same breath-hold as the gas MRI. The feasibility of using this technique for regional quantification of ventilation of specific pulmonary structures is demonstrated for the lobes.The direct and indirect methods of hyperpolarized gas MRI to CT image registration were compared using lung images from 15 asthma patients. Both affine and diffeomorphic image transformations were implemented. Registration accuracy was evaluated using the target registration error (TRE) of anatomical landmarks identified on (1)H MRI and CT. The Wilcoxon signed-rank test was used to test statistical significance.For the affine transformation, the indirect method of image registration was significantly more accurate than the direct method (TRE = 14.7 ± 3.2 versus 19.6 ± 12.7 mm, p = 0.036). Using a deformable transformation, the indirect method was also more accurate than the direct method (TRE = 13.5 ± 3.3 versus 20.4 ± 12.8 mm, p = 0.006).Accurate image registration is critical for quantification of regional lung ventilation with hyperpolarized gas MRI within the anatomy delineated by CT. Automatic deformable image registration of hyperpolarized gas MRI to CT via same breath-hold (1)H MRI is more accurate than direct registration. Potential applications include improved multi-modality image fusion, functionally weighted radiotherapy planning, and quantification of

  11. Methods for determining the genetic affinity of microorganisms and viruses

    NASA Technical Reports Server (NTRS)

    Fox, George E. (Inventor); Willson, III, Richard C. (Inventor); Zhang, Zhengdong (Inventor)

    2012-01-01

    Selecting which sub-sequences in a database of nucleic acid such as 16S rRNA are highly characteristic of particular groupings of bacteria, microorganisms, fungi, etc. on a substantially phylogenetic tree. Also applicable to viruses comprising viral genomic RNA or DNA. A catalogue of highly characteristic sequences identified by this method is assembled to establish the genetic identity of an unknown organism. The characteristic sequences are used to design nucleic acid hybridization probes that include the characteristic sequence or its complement, or are derived from one or more characteristic sequences. A plurality of these characteristic sequences is used in hybridization to determine the phylogenetic tree position of the organism(s) in a sample. Those target organisms represented in the original sequence database and sufficient characteristic sequences can identify to the species or subspecies level. Oligonucleotide arrays of many probes are especially preferred. A hybridization signal can comprise fluorescence, chemiluminescence, or isotopic labeling, etc.; or sequences in a sample can be detected by direct means, e.g. mass spectrometry. The method's characteristic sequences can also be used to design specific PCR primers. The method uniquely identifies the phylogenetic affinity of an unknown organism without requiring prior knowledge of what is present in the sample. Even if the organism has not been previously encountered, the method still provides useful information about which phylogenetic tree bifurcation nodes encompass the organism.

  12. Warped document image correction method based on heterogeneous registration strategies

    NASA Astrophysics Data System (ADS)

    Tong, Lijing; Zhan, Guoliang; Peng, Quanyao; Li, Yang; Li, Yifan

    2013-03-01

    With the popularity of digital camera and the application requirement of digitalized document images, using digital cameras to digitalize document images has become an irresistible trend. However, the warping of the document surface impacts on the quality of the Optical Character Recognition (OCR) system seriously. To improve the warped document image's vision quality and the OCR rate, this paper proposed a warped document image correction method based on heterogeneous registration strategies. This method mosaics two warped images of the same document from different viewpoints. Firstly, two feature points are selected from one image. Then the two feature points are registered in the other image base on heterogeneous registration strategies. At last, image mosaics are done for the two images, and the best mosaiced image is selected by OCR recognition results. As a result, for the best mosaiced image, the distortions are mostly removed and the OCR results are improved markedly. Experimental results show that the proposed method can resolve the issue of warped document image correction more effectively.

  13. Intensity based methods for brain MRI longitudinal registration. A study on multiple sclerosis patients.

    PubMed

    Diez, Yago; Oliver, Arnau; Cabezas, Mariano; Valverde, Sergi; Martí, Robert; Vilanova, Joan Carles; Ramió-Torrentà, Lluís; Rovira, Alex; Lladó, Xavier

    2014-07-01

    Registration is a key step in many automatic brain Magnetic Resonance Imaging (MRI) applications. In this work we focus on longitudinal registration of brain MRI for Multiple Sclerosis (MS) patients. First of all, we analyze the effect that MS lesions have on registration by synthetically eliminating some of the lesions. Our results show how a widely used method for longitudinal registration such as rigid registration is practically unconcerned by the presence of MS lesions while several non-rigid registration methods produce outputs that are significantly different. We then focus on assessing which is the best registration method for longitudinal MRI images of MS patients. In order to analyze the results obtained for all studied criteria, we use both descriptive statistics and statistical inference: one way ANOVA, pairwise t-tests and permutation tests. PMID:24338728

  14. PDZ Affinity Chromatography: A general method for affinity purification of proteins based on PDZ domains and their ligands

    PubMed Central

    Walkup, Ward G.; Kennedy, Mary B.

    2014-01-01

    PDZ (PSD-95, DiscsLarge, ZO1) domains function in nature as protein binding domains within scaffold and membrane-associated proteins. They comprise ~ 90 residues and make specific, high affinity interactions with complementary C-terminal peptide sequences, with other PDZ domains, and with phospholipids. We hypothesized that the specific, strong interactions of PDZ domains with their ligands would make them well suited for use in affinity chromatography. Here we describe a novel affinity chromatography method applicable for the purification of proteins that contain PDZ domain-binding ligands, either naturally or introduced by genetic engineering. We created a series of affinity resins comprised of PDZ domains from the scaffold protein PSD-95, or from neuronal nitric oxide synthase (nNOS), coupled to solid supports. We used them to purify heterologously expressed neuronal proteins or protein domains containing endogenous PDZ domain ligands, eluting the proteins with free PDZ domain peptide ligands. We show that Proteins of Interest (POIs) lacking endogenous PDZ domain ligands can be engineered as fusion products containing C-terminal PDZ domain ligand peptides or internal, N- or C-terminal PDZ domains and then can be purified by the same method. Using this method, we recovered recombinant GFP fused to a PDZ-domain ligand in active form as verified by fluorescence yield. Similarly, chloramphenicol acetyltransferase (CAT) and β-Galactosidase (LacZ) fused to a C-terminal PDZ domain ligand or an N-terminal PDZ domain were purified in active form as assessed by enzymatic assay. In general, PDZ domains and ligands derived from PSD-95 were superior to those from nNOS for this method. PDZ Domain Affinity Chromatography promises to be a versatile and effective method for purification of a wide variety of natural and recombinant proteins. PMID:24607360

  15. A fast alignment method for breast MRI follow-up studies using automated breast segmentation and current-prior registration

    NASA Astrophysics Data System (ADS)

    Wang, Lei; Strehlow, Jan; Rühaak, Jan; Weiler, Florian; Diez, Yago; Gubern-Merida, Albert; Diekmann, Susanne; Laue, Hendrik; Hahn, Horst K.

    2015-03-01

    In breast cancer screening for high-risk women, follow-up magnetic resonance images (MRI) are acquired with a time interval ranging from several months up to a few years. Prior MRI studies may provide additional clinical value when examining the current one and thus have the potential to increase sensitivity and specificity of screening. To build a spatial correlation between suspicious findings in both current and prior studies, a reliable alignment method between follow-up studies is desirable. However, long time interval, different scanners and imaging protocols, and varying breast compression can result in a large deformation, which challenges the registration process. In this work, we present a fast and robust spatial alignment framework, which combines automated breast segmentation and current-prior registration techniques in a multi-level fashion. First, fully automatic breast segmentation is applied to extract the breast masks that are used to obtain an initial affine transform. Then, a non-rigid registration algorithm using normalized gradient fields as similarity measure together with curvature regularization is applied. A total of 29 subjects and 58 breast MR images were collected for performance assessment. To evaluate the global registration accuracy, the volume overlap and boundary surface distance metrics are calculated, resulting in an average Dice Similarity Coefficient (DSC) of 0.96 and root mean square distance (RMSD) of 1.64 mm. In addition, to measure local registration accuracy, for each subject a radiologist annotated 10 pairs of markers in the current and prior studies representing corresponding anatomical locations. The average distance error of marker pairs dropped from 67.37 mm to 10.86 mm after applying registration.

  16. SU-E-J-196: New Visualization Methods for Longitudinal MRI Registrations and Segmentations

    SciTech Connect

    Veeraraghavan, H; Deasy, J

    2014-06-01

    Purpose: To develop visualization techniques to facilitate easy assessment of (a) registration and (b) tracking volumetric changes in structures during radiation therapy from MRI. Method: The frequently used method for visualizing registrations between scans is a multi-color overlay technique or deformation vector fields. However, the overlay technique is unintuitive and does not help to appreciate the quality of registration particularly when the registration mismatches are not very large. Similarly, the deformation fields give an indication of extent of deformation but do not help to assess the differences in registration. We present a mirroring and edge-augmented mirroring technique that places the fixed and moving image next to each other and allows the user to quickly assess the small differences in registration. Next, we present a volumetric intersection based 3D model to visualize the changes in diseased lymph node volumes in head and neck cancer. 3D model-based visualization provides more information about the location-specific changes in volume rather than the simplistic one dimensional information obtained from 2D plot of nodal volume changes. Result: We show results comparing our approach with the standard colorbased overlay method for comparing registrations of intra-patient registrations using T2-MRI. Upon comparing the mirroring technique with the color-overlay, one can more easily appreciate the differences in registration. Adding edge-based mirroring seems to further assist in evaluating the registration. Our approach for viewing registrations seems to be more intuitive and easy to use in order to help assess the quality of registration compared to color-based overlays. Similarly, the change volumetric model together with a 2D plot reveals more information including the locations undergoing changes and responding to treatment. Conclusions: Better approaches are necessary for assessing the quality of registrations and changes in diseased structures

  17. An Innovative Class Registration Method Based on Bar Code Input.

    ERIC Educational Resources Information Center

    Freeman, Raoul J.

    1983-01-01

    Describes system of computerized class registration utilizing bar code input which is part of the Student Data System, developed by Management Information Division of the Los Angeles Unified School District. An explanation of the system notes the hardware used, printing of bar code labels, registration procedures, and operational aspects. (EJS)

  18. Development and application of pulmonary structure-function registration methods: towards pulmonary image-guidance tools for improved airway targeted therapies and outcomes

    NASA Astrophysics Data System (ADS)

    Guo, Fumin; Pike, Damien; Svenningsen, Sarah; Coxson, Harvey O.; Drozd, John J.; Yuan, Jing; Fenster, Aaron; Parraga, Grace

    2014-03-01

    Objectives: We aimed to develop a way to rapidly generate multi-modality (MRI-CT) pulmonary imaging structurefunction maps using novel non-rigid image registration methods. This objective is part of our overarching goal to provide an image processing pipeline to generate pulmonary structure-function maps and guide airway-targeted therapies. Methods: Anatomical 1H and functional 3He MRI were acquired in 5 healthy asymptomatic ex-smokers and 7 ex-smokers with chronic obstructive pulmonary disease (COPD) at inspiration breath-hold. Thoracic CT was performed within ten minutes of MRI using the same breath-hold volume. Landmark-based affine registration methods previously validated for imaging of COPD, was based on corresponding fiducial markers located in both CT and 1H MRI coronal slices and compared with shape-based CT-MRI non-rigid registration. Shape-based CT-MRI registration was developed by first identifying the shapes of the lung cavities manually, and then registering the two shapes using affine and thin-plate spline algorithms. We compared registration accuracy using the fiducial localization error (FLE) and target registration error (TRE). Results: For landmark-based registration, the TRE was 8.4±5.3 mm for whole lung and 7.8±4.6 mm for the R and L lungs registered independently (p=0.4). For shape-based registration, the TRE was 8.0±4.6 mm for whole lung as compared to 6.9±4.4 mm for the R and L lung registered independently and this difference was significant (p=0.01). The difference for shape-based (6.9±4.4 mm) and landmark-based R and L lung registration (7.8±4.6 mm) was also significant (p=.04) Conclusion: Shape-based registration TRE was significantly improved compared to landmark-based registration when considering L and R lungs independently.

  19. Selective high affinity polydentate ligands and methods of making such

    SciTech Connect

    DeNardo, Sally; DeNardo, Gerald; Balhorn, Rodney

    2010-02-16

    This invention provides novel polydentate selective high affinity ligands (SHALs) that can be used in a variety of applications in a manner analogous to the use of antibodies. SHALs typically comprise a multiplicity of ligands that each bind different region son the target molecule. The ligands are joined directly or through a linker thereby forming a polydentate moiety that typically binds the target molecule with high selectivity and avidity.

  20. Digital image registration method based upon binary boundary maps

    NASA Technical Reports Server (NTRS)

    Jayroe, R. R., Jr.; Andrus, J. F.; Campbell, C. W.

    1974-01-01

    A relatively fast method is presented for matching or registering the digital data of imagery from the same ground scene acquired at different times, or from different multispectral images, sensors, or both. It is assumed that the digital images can be registed by using translations and rotations only, that the images are of the same scale, and that little or no distortion exists between images. It is further assumed that by working with several local areas of the image, the rotational effects in the local areas can be neglected. Thus, by treating the misalignments of local areas as translations, it is possible to determine rotational and translational misalignments for a larger portion of the image containing the local areas. This procedure of determining the misalignment and then registering the data according to the misalignment can be repeated until the desired degree of registration is achieved. The method to be presented is based upon the use of binary boundary maps produced from the raw digital imagery rather than the raw digital data.

  1. 3D-2D registration of cerebral angiograms: a method and evaluation on clinical images.

    PubMed

    Mitrovic, Uroš; Špiclin, Žiga; Likar, Boštjan; Pernuš, Franjo

    2013-08-01

    Endovascular image-guided interventions (EIGI) involve navigation of a catheter through the vasculature followed by application of treatment at the site of anomaly using live 2D projection images for guidance. 3D images acquired prior to EIGI are used to quantify the vascular anomaly and plan the intervention. If fused with the information of live 2D images they can also facilitate navigation and treatment. For this purpose 3D-2D image registration is required. Although several 3D-2D registration methods for EIGI achieve registration accuracy below 1 mm, their clinical application is still limited by insufficient robustness or reliability. In this paper, we propose a 3D-2D registration method based on matching a 3D vasculature model to intensity gradients of live 2D images. To objectively validate 3D-2D registration methods, we acquired a clinical image database of 10 patients undergoing cerebral EIGI and established "gold standard" registrations by aligning fiducial markers in 3D and 2D images. The proposed method had mean registration accuracy below 0.65 mm, which was comparable to tested state-of-the-art methods, and execution time below 1 s. With the highest rate of successful registrations and the highest capture range the proposed method was the most robust and thus a good candidate for application in EIGI. PMID:23649179

  2. A comparison of seven methods of within-subjects rigid-body pedobarographic image registration.

    PubMed

    Pataky, Todd C; Goulermas, John Y; Crompton, Robin H

    2008-10-20

    Image registration, the process of transforming images such that homologous structures optimally overlap, provides the pre-processing foundation for pixel-level functional image analysis. The purpose of this study was to compare the performances of seven methods of within-subjects pedobarographic image registration: (1) manual, (2) principal axes, (3) centre of pressure trajectory, (4) mean squared error, (5) probability-weighted variance, (6) mutual information, and (7) exclusive OR. We assumed that foot-contact geometry changes were negligibly small trial-to-trial and thus that a rigid-body transformation could yield optimum registration performance. Thirty image pairs were randomly selected from our laboratory database and were registered using each method. To compensate for inter-rater variability, the mean registration parameters across 10 raters were taken as representative of manual registration. Registration performance was assessed using four dissimilarity metrics (#4-7 above). One-way MANOVA found significant differences between the methods (p<0.001). Bonferroni post-hoc tests revealed that the centre of pressure method performed the poorest (p<0.001) and that the principal axes method tended to perform more poorly than remaining methods (p<0.070). Average manual registration was not different from the remaining methods (p=1.000). The results suggest that a variety of linear registration methods are appropriate for within-subjects pedobarographic images, and that manual image registration is a viable alternative to algorithmic registration when parameters are averaged across raters. The latter finding, in particular, may be useful for cases of image peculiarities resulting from outlier trials or from experimental manipulations that induce substantial changes in contact area or pressure profile geometry. PMID:18790481

  3. Data on the verification and validation of segmentation and registration methods for diffusion MRI.

    PubMed

    Esteban, Oscar; Zosso, Dominique; Daducci, Alessandro; Bach-Cuadra, Meritxell; Ledesma-Carbayo, María J; Thiran, Jean-Philippe; Santos, Andres

    2016-09-01

    The verification and validation of segmentation and registration methods is a necessary assessment in the development of new processing methods. However, verification and validation of diffusion MRI (dMRI) processing methods is challenging for the lack of gold-standard data. The data described here are related to the research article entitled "Surface-driven registration method for the structure-informed segmentation of diffusion MR images" [1], in which publicly available data are used to derive golden-standard reference-data to validate and evaluate segmentation and registration methods in dMRI. PMID:27508235

  4. Comparative study of multimodal intra-subject image registration methods on a publicly available database

    NASA Astrophysics Data System (ADS)

    Miri, Mohammad Saleh; Ghayoor, Ali; Johnson, Hans J.; Sonka, Milan

    2016-03-01

    This work reports on a comparative study between five manual and automated methods for intra-subject pair-wise registration of images from different modalities. The study includes a variety of inter-modal image registrations (MR-CT, PET-CT, PET-MR) utilizing different methods including two manual point-based techniques using rigid and similarity transformations, one automated point-based approach based on Iterative Closest Point (ICP) algorithm, and two automated intensity-based methods using mutual information (MI) and normalized mutual information (NMI). These techniques were employed for inter-modal registration of brain images of 9 subjects from a publicly available dataset, and the results were evaluated qualitatively via checkerboard images and quantitatively using root mean square error and MI criteria. In addition, for each inter-modal registration, a paired t-test was performed on the quantitative results in order to find any significant difference between the results of the studied registration techniques.

  5. An Automatic Optical and SAR Image Registration Method Using Iterative Multi-Level and Refinement Model

    NASA Astrophysics Data System (ADS)

    Xu, C.; Sui, H. G.; Li, D. R.; Sun, K. M.; Liu, J. Y.

    2016-06-01

    Automatic image registration is a vital yet challenging task, particularly for multi-sensor remote sensing images. Given the diversity of the data, it is unlikely that a single registration algorithm or a single image feature will work satisfactorily for all applications. Focusing on this issue, the mainly contribution of this paper is to propose an automatic optical-to-SAR image registration method using -level and refinement model: Firstly, a multi-level strategy of coarse-to-fine registration is presented, the visual saliency features is used to acquire coarse registration, and then specific area and line features are used to refine the registration result, after that, sub-pixel matching is applied using KNN Graph. Secondly, an iterative strategy that involves adaptive parameter adjustment for re-extracting and re-matching features is presented. Considering the fact that almost all feature-based registration methods rely on feature extraction results, the iterative strategy improve the robustness of feature matching. And all parameters can be automatically and adaptively adjusted in the iterative procedure. Thirdly, a uniform level set segmentation model for optical and SAR images is presented to segment conjugate features, and Voronoi diagram is introduced into Spectral Point Matching (VSPM) to further enhance the matching accuracy between two sets of matching points. Experimental results show that the proposed method can effectively and robustly generate sufficient, reliable point pairs and provide accurate registration.

  6. A hybrid biomechanical model-based image registration method for sliding objects

    NASA Astrophysics Data System (ADS)

    Han, Lianghao; Hawkes, David; Barratt, Dean

    2014-03-01

    The sliding motion between two anatomic structures, such as lung against chest wall, liver against surrounding tissues, produces a discontinuous displacement field between their boundaries. Capturing the sliding motion is quite challenging for intensity-based image registration methods in which a smoothness condition has commonly been applied to ensure the deformation consistency of neighborhood voxels. Such a smoothness constraint contradicts motion physiology at the boundaries of these anatomic structures. Although various regularisation schemes have been developed to handle sliding motion under the framework of non-rigid intensity-based image registration, the recovered displacement field may still not be physically plausible. In this study, a new framework that incorporates a patient-specific biomechanical model with a non-rigid image registration scheme for motion estimation of sliding objects has been developed. The patient-specific model provides the motion estimation with an explicit simulation of sliding motion, while the subsequent non-rigid image registration compensates for smaller residuals of the deformation due to the inaccuracy of the physical model. The algorithm was tested against the results of the published literature using 4D CT data from 10 lung cancer patients. The target registration error (TRE) of 3000 landmarks with the proposed method (1.37+/-0.89 mm) was significantly lower than that with the popular B-spline based free form deformation (FFD) registration (4.5+/-3.9 mm), and was smaller than that using the B-spline based FFD registration with the sliding constraint (1.66+/-1.14 mm) or using the B-spline based FFD registration on segmented lungs (1.47+/-1.1 mm). A paired t-test showed that the improvement of registration performance with the proposed method was significant (p<0.01). The propose method also achieved the best registration performance on the landmarks near lung surfaces. Since biomechanical models captured most of the lung

  7. [Registration of accidents and injuries in primary health care. Methods and the users' experiences].

    PubMed

    Lund, H; Lium, E

    1997-11-10

    The registration of accidents and injuries in primary health care is inadequate. One of the reasons for this inadequacy is most certainly lack of enthusiasm although lack of to-the-point registration methods is just as much to blame. We have used an automatic accident registration mode in the PC programme Profdoc. This accident registration programme is very useful and time cost-effective. In Os municipality, where the registration took place in 1996, the results have proved to be very helpful in accident prevention. Nevertheless, the programme still needs EDB-knowledgeable doctors, to collect the data. In the near future it will hopefully be possible to feed the raw material to a server, which would then organize the data. This would provide general practitioners with a completed report in exchange for raw material. PMID:9441426

  8. Tracking and registration method based on vector operation for augmented reality system

    NASA Astrophysics Data System (ADS)

    Gao, Yanfei; Wang, Hengyou; Bian, Xiaoning

    2015-08-01

    Tracking and registration is one key issue for an augmented reality (AR) system. For the marker-based AR system, the research focuses on detecting the real-time position and orientation of camera. In this paper, we describe a method of tracking and registration using the vector operations. Our method is proved to be stable and accurate, and have a good real-time performance.

  9. A nonlinear biomechanical model based registration method for aligning prone and supine MR breast images.

    PubMed

    Han, Lianghao; Hipwell, John H; Eiben, Björn; Barratt, Dean; Modat, Marc; Ourselin, Sebastien; Hawkes, David J

    2014-03-01

    Preoperative diagnostic magnetic resonance (MR) breast images can provide good contrast between different tissues and 3-D information about suspicious tissues. Aligning preoperative diagnostic MR images with a patient in the theatre during breast conserving surgery could assist surgeons in achieving the complete excision of cancer with sufficient margins. Typically, preoperative diagnostic MR breast images of a patient are obtained in the prone position, while surgery is performed in the supine position. The significant shape change of breasts between these two positions due to gravity loading, external forces and related constraints makes the alignment task extremely difficult. Our previous studies have shown that either nonrigid intensity-based image registration or biomechanical modelling alone are limited in their ability to capture such a large deformation. To tackle this problem, we proposed in this paper a nonlinear biomechanical model-based image registration method with a simultaneous optimization procedure for both the material parameters of breast tissues and the direction of the gravitational force. First, finite element (FE) based biomechanical modelling is used to estimate a physically plausible deformation of the pectoral muscle and the major deformation of breast tissues due to gravity loading. Then, nonrigid intensity-based image registration is employed to recover the remaining deformation that FE analyses do not capture due to the simplifications and approximations of biomechanical models and the uncertainties of external forces and constraints. We assess the registration performance of the proposed method using the target registration error of skin fiducial markers and the Dice similarity coefficient (DSC) of fibroglandular tissues. The registration results on prone and supine MR image pairs are compared with those from two alternative nonrigid registration methods for five breasts. Overall, the proposed algorithm achieved the best registration

  10. Affinity measurement of single chain antibodies: a mathematical method facilitated by statistical software SigmaPlot.

    PubMed

    Safdari, Yaghoub; Farajnia, Safar; Asgharzadeh, Mohammad; Khalili, Masoumeh; Jaliani, Hossein Zarei

    2014-02-01

    Because they are monovalent for antigen, single chain antibodies display a different antibody-antigen interaction pattern from that of full-length antibodies. Using the law of mass action and considering the antibody-antigen binding pattern at OD-100% and OD-50% points, we introduced a formula for estimating single chain antibody affinity. Sigmoid curves of optical density values versus antibody concentrations were drawn and used to determine antibody concentrations at OD-50% points using statistical software SigmaPlot. The OD-50% points were then used to calculate the affinity via the mathematical formula. A software-adapted format of the equation is also presented for further facilitation of the calculation process. The accuracy of this method for affinity calculation was proved by surface plasma resonance. This method offers a precise evaluation of antibody affinity without requiring special material or apparatus, making it possible to be performed in any biological laboratory with minimum facilities. PMID:24555931

  11. Robust methods for automatic image-to-world registration in cone-beam CT interventional guidance

    PubMed Central

    Dang, H.; Otake, Y.; Schafer, S.; Stayman, J. W.; Kleinszig, G.; Siewerdsen, J. H.

    2012-01-01

    Purpose: Real-time surgical navigation relies on accurate image-to-world registration to align the coordinate systems of the image and patient. Conventional manual registration can present a workflow bottleneck and is prone to manual error and intraoperator variability. This work reports alternative means of automatic image-to-world registration, each method involving an automatic registration marker (ARM) used in conjunction with C-arm cone-beam CT (CBCT). The first involves a Known-Model registration method in which the ARM is a predefined tool, and the second is a Free-Form method in which the ARM is freely configurable. Methods: Studies were performed using a prototype C-arm for CBCT and a surgical tracking system. A simple ARM was designed with markers comprising a tungsten sphere within infrared reflectors to permit detection of markers in both x-ray projections and by an infrared tracker. The Known-Model method exercised a predefined specification of the ARM in combination with 3D-2D registration to estimate the transformation that yields the optimal match between forward projection of the ARM and the measured projection images. The Free-Form method localizes markers individually in projection data by a robust Hough transform approach extended from previous work, backprojected to 3D image coordinates based on C-arm geometric calibration. Image-domain point sets were transformed to world coordinates by rigid-body point-based registration. The robustness and registration accuracy of each method was tested in comparison to manual registration across a range of body sites (head, thorax, and abdomen) of interest in CBCT-guided surgery, including cases with interventional tools in the radiographic scene. Results: The automatic methods exhibited similar target registration error (TRE) and were comparable or superior to manual registration for placement of the ARM within ∼200 mm of C-arm isocenter. Marker localization in projection data was robust across all

  12. Robust methods for automatic image-to-world registration in cone-beam CT interventional guidance

    SciTech Connect

    Dang, H.; Otake, Y.; Schafer, S.; Stayman, J. W.; Kleinszig, G.; Siewerdsen, J. H.

    2012-10-15

    Purpose: Real-time surgical navigation relies on accurate image-to-world registration to align the coordinate systems of the image and patient. Conventional manual registration can present a workflow bottleneck and is prone to manual error and intraoperator variability. This work reports alternative means of automatic image-to-world registration, each method involving an automatic registration marker (ARM) used in conjunction with C-arm cone-beam CT (CBCT). The first involves a Known-Model registration method in which the ARM is a predefined tool, and the second is a Free-Form method in which the ARM is freely configurable. Methods: Studies were performed using a prototype C-arm for CBCT and a surgical tracking system. A simple ARM was designed with markers comprising a tungsten sphere within infrared reflectors to permit detection of markers in both x-ray projections and by an infrared tracker. The Known-Model method exercised a predefined specification of the ARM in combination with 3D-2D registration to estimate the transformation that yields the optimal match between forward projection of the ARM and the measured projection images. The Free-Form method localizes markers individually in projection data by a robust Hough transform approach extended from previous work, backprojected to 3D image coordinates based on C-arm geometric calibration. Image-domain point sets were transformed to world coordinates by rigid-body point-based registration. The robustness and registration accuracy of each method was tested in comparison to manual registration across a range of body sites (head, thorax, and abdomen) of interest in CBCT-guided surgery, including cases with interventional tools in the radiographic scene. Results: The automatic methods exhibited similar target registration error (TRE) and were comparable or superior to manual registration for placement of the ARM within {approx}200 mm of C-arm isocenter. Marker localization in projection data was robust across all

  13. Robust registration method for interventional MRI-guided thermal ablation of prostate cancer

    NASA Astrophysics Data System (ADS)

    Fei, Baowei; Wheaton, Andrew; Lee, Zhenghong; Nagano, Kenichi; Duerk, Jeffrey L.; Wilson, David L.

    2001-05-01

    We are investigating methods to register live-time interventional magnetic resonance imaging (iMRI) slice images with a previously obtained, high resolution MRI image volume. The immediate application is for iMRI-guided treatments of prostate cancer. We created and evaluated a slice-to-volume mutual information registration algorithm for MR images with special features to improve robustness. Features included a multi-resolution approach and automatic restarting to avoid local minima. We acquired 3D volume images from a 1.5 T MRI system and simulated iMRI images. To assess the quality of registration, we calculated 3D displacement on a voxel-by-voxel basis over a volume of interest between slice-to-volume registration and volume-to- volume registrations that were previously shown to be quite accurate. More than 500 registration experiments were performed on MR images of volunteers. The slice-to-volume registration algorithm was very robust for transverse images covering the prostate. A 100% success rate was achieved with an acceptance criterion of <1.0 mm displacement error over the prostate. Our automatic slice-to-volume mutual information registration algorithm is robust and probably sufficiently accurate to aid in the application of iMRI- guided thermal ablation of prostate cancer.

  14. The heritability of the functional connectome is robust to common nonlinear registration methods

    NASA Astrophysics Data System (ADS)

    Hafzalla, George W.; Prasad, Gautam; Baboyan, Vatche G.; Faskowitz, Joshua; Jahanshad, Neda; McMahon, Katie L.; de Zubicaray, Greig I.; Wright, Margaret J.; Braskie, Meredith N.; Thompson, Paul M.

    2016-03-01

    Nonlinear registration algorithms are routinely used in brain imaging, to align data for inter-subject and group comparisons, and for voxelwise statistical analyses. To understand how the choice of registration method affects maps of functional brain connectivity in a sample of 611 twins, we evaluated three popular nonlinear registration methods: Advanced Normalization Tools (ANTs), Automatic Registration Toolbox (ART), and FMRIB's Nonlinear Image Registration Tool (FNIRT). Using both structural and functional MRI, we used each of the three methods to align the MNI152 brain template, and 80 regions of interest (ROIs), to each subject's T1-weighted (T1w) anatomical image. We then transformed each subject's ROIs onto the associated resting state functional MRI (rs-fMRI) scans and computed a connectivity network or functional connectome for each subject. Given the different degrees of genetic similarity between pairs of monozygotic (MZ) and same-sex dizygotic (DZ) twins, we used structural equation modeling to estimate the additive genetic influences on the elements of the function networks, or their heritability. The functional connectome and derived statistics were relatively robust to nonlinear registration effects.

  15. Self-Registration Methods for Increasing Membrane Utilization within Compression-Sealed Microchannel Hemodialysers

    PubMed Central

    Paul, Brian K.; Porter, Spencer D.

    2015-01-01

    More than 1.2 million people worldwide require regular hemodialysis therapy to treat end stage renal failure. Current hemodialysis systems are too expensive to support at-home hemodialysis where more frequent and longer duration treatment can lead to better patient outcomes. The key cost driver for hemodialysers is the cost of the hemodialysis membrane. Microchannel hemodialysers are smaller providing the potential to use significantly less membrane. Prior work has demonstrated the use of sealing bosses to form compression seals in microchannel hemodialysers. In this paper, estimates show that the percentage of the membrane utilized for mass transfer is highly dependent on the design and registration accuracy of adjacent blood and dialysate laminae. Efforts here focus on the development of a self-registration method to align polycarbonate laminae compatible with compression sealing schemes for membrane separation applications. Self-nesting registration methods were demonstrated with average registration accuracies of 11.4 ± 7.2 μm measured over a 50 mm scale. Analysis shows that the registration accuracy is constrained by tolerances in the embossing process. A dialysis test article was produced using the self-nesting registration method showing a measured average one-dimensional misregistration of 18.5 μm allowing a potential 41.4% of the membrane to be utilized for mass transfer when considering both microchannel and header regions. Mass transfer results provide evidence of a twofold to threefold increase in membrane utilization over other designs in the existing literature. PMID:25642151

  16. A method of image registration for small animal, multi-modality imaging.

    PubMed

    Chow, Patrick L; Stout, David B; Komisopoulou, Evangelia; Chatziioannou, Arion F

    2006-01-21

    Many research institutions have a full suite of preclinical tomographic scanners to answer biomedical questions in vivo. Routine multi-modality imaging requires robust registration of images generated by various tomographs. We have implemented a hardware registration method for preclinical imaging that is similar to that used in the combined positron emission tomography (PET)/computed tomography (CT) scanners in the clinic. We designed an imaging chamber which can be rigidly and reproducibly mounted on separate microPET and microCT scanners. We have also designed a three-dimensional grid phantom with 1288 lines that is used to generate the spatial transformation matrix from software registration using a 15-parameter perspective model. The imaging chamber works in combination with the registration phantom synergistically to achieve the image registration goal. We verified that the average registration error between two imaging modalities is 0.335 mm using an in vivo mouse bone scan. This paper also estimates the impact of image misalignment on PET quantitation using attenuation corrections generated from misregistered images. Our technique is expected to produce PET quantitation errors of less than 5%. The methods presented are robust and appropriate for routine use in high throughput animal imaging facilities. PMID:16394345

  17. Automatic registration method for multisensor datasets adopted for dimensional measurements on cutting tools

    NASA Astrophysics Data System (ADS)

    Shaw, L.; Ettl, S.; Mehari, F.; Weckenmann, A.; Häusler, G.

    2013-04-01

    Multisensor systems with optical 3D sensors are frequently employed to capture complete surface information by measuring workpieces from different views. During coarse and fine registration the resulting datasets are afterward transformed into one common coordinate system. Automatic fine registration methods are well established in dimensional metrology, whereas there is a deficit in automatic coarse registration methods. The advantage of a fully automatic registration procedure is twofold: it enables a fast and contact-free alignment and further a flexible application to datasets of any kind of optical 3D sensor. In this paper, an algorithm adapted for a robust automatic coarse registration is presented. The method was originally developed for the field of object reconstruction or localization. It is based on a segmentation of planes in the datasets to calculate the transformation parameters. The rotation is defined by the normals of three corresponding segmented planes of two overlapping datasets, while the translation is calculated via the intersection point of the segmented planes. First results have shown that the translation is strongly shape dependent: 3D data of objects with non-orthogonal planar flanks cannot be registered with the current method. In the novel supplement for the algorithm, the translation is additionally calculated via the distance between centroids of corresponding segmented planes, which results in more than one option for the transformation. A newly introduced measure considering the distance between the datasets after coarse registration evaluates the best possible transformation. Results of the robust automatic registration method are presented on the example of datasets taken from a cutting tool with a fringe-projection system and a focus-variation system. The successful application in dimensional metrology is proven with evaluations of shape parameters based on the registered datasets of a calibrated workpiece.

  18. Evaluation and validation methods for intersubject nonrigid 3D image registration of the human brain

    NASA Astrophysics Data System (ADS)

    Guo, Ting; Starreveld, Yves P.; Peters, Terry M.

    2005-04-01

    This work presents methodologies for assessing the accuracy of non-rigid intersubject registration algorithms from both qualitative and quantitative perspectives. The first method was based on a set of 43 anatomical landmarks. MRI brain images of 12 subjects were non-rigidly registered to the standard MRI dataset. The "gold-standard" coordinates of the 43 landmarks in the target were estimated by averaging their coordinates after 6 tagging sessions. The Euclidean distance between each landmark of a subject after warping to the reference space and the homologous "gold-standard" landmark on the reference image was considered as the registration error. Another method based on visual inspection software displaying the spatial change of colour-coded spheres, before and after warping, was also developed to evaluate the performance of the non-rigid warping algorithms within the homogeneous regions in the deep-brain. Our methods were exemplified by assessing and comparing the accuracy of two intersubject non-rigid registration approaches, AtamaiWarp and ANIMAL algorithms. From the first method, the average registration error was 1.04mm +/- 0.65mm for AtamaiWarp, and 1.59mm +/- 1.47mm for ANIMAL. With maximum registration errors of 2.78mm and 3.90mm respectively, AtamaiWarp and ANIMAL located 58% and 35% landmarks respectively with registration errors less than 1mm. A paired t-test showed that the differences in registration error between AtamaiWarp and ANIMAL were significant (P < 0.002) demonstrating that AtamaiWarp, in addition to being over 60 times faster than ANIMAL, also provides more accurate results. From the second method, both algorithms treated the interior of homogeneous regions in an appropriate manner.

  19. A faster method for 3D/2D medical image registration--a simulation study.

    PubMed

    Birkfellner, Wolfgang; Wirth, Joachim; Burgstaller, Wolfgang; Baumann, Bernard; Staedele, Harald; Hammer, Beat; Gellrich, Niels Claudius; Jacob, Augustinus Ludwig; Regazzoni, Pietro; Messmer, Peter

    2003-08-21

    3D/2D patient-to-computed-tomography (CT) registration is a method to determine a transformation that maps two coordinate systems by comparing a projection image rendered from CT to a real projection image. Iterative variation of the CT's position between rendering steps finally leads to exact registration. Applications include exact patient positioning in radiation therapy, calibration of surgical robots, and pose estimation in computer-aided surgery. One of the problems associated with 3D/2D registration is the fact that finding a registration includes solving a minimization problem in six degrees of freedom (dof) in motion. This results in considerable time requirements since for each iteration step at least one volume rendering has to be computed. We show that by choosing an appropriate world coordinate system and by applying a 2D/2D registration method in each iteration step, the number of iterations can be grossly reduced from n6 to n5. Here, n is the number of discrete variations around a given coordinate. Depending on the configuration of the optimization algorithm, this reduces the total number of iterations necessary to at least 1/3 of it's original value. The method was implemented and extensively tested on simulated x-ray images of a tibia, a pelvis and a skull base. When using one projective image and a discrete full parameter space search for solving the optimization problem, average accuracy was found to be 1.0 +/- 0.6(degrees) and 4.1 +/- 1.9 (mm) for a registration in six parameters, and 1.0 +/- 0.7(degrees) and 4.2 +/- 1.6 (mm) when using the 5 + 1 dof method described in this paper. Time requirements were reduced by a factor 3.1. We conclude that this hardware-independent optimization of 3D/2D registration is a step towards increasing the acceptance of this promising method for a wide number of clinical applications. PMID:12974581

  20. Lung texture in serial thoracic CT scans: Registration-based methods to compare anatomically matched regions1

    PubMed Central

    Cunliffe, Alexandra R.; Armato, Samuel G.; Fei, Xianhan M.; Tuohy, Rachel E.; Al-Hallaq, Hania A.

    2013-01-01

    Purpose: The aim of this study was to compare three demons registration-based methods to identify spatially matched regions in serial computed tomography (CT) scans for use in texture analysis. Methods: Two thoracic CT scans containing no lung abnormalities and acquired during serial examinations separated by at least one week were retrospectively collected from 27 patients. Over 1000 regions of interest (ROIs) were randomly placed in the lungs of each baseline scan. Anatomically matched ROIs in the corresponding follow-up scan were placed by mapping the baseline scan ROI center pixel to (1) the original follow-up scan, (2) the follow-up scan resampled to match the baseline scan voxel size, and (3) the follow-up scan aligned to the baseline scan through affine registration. Mappings used the vector field obtained through demons deformable registration of each follow-up scan variant to the baseline scan. 140 texture features distributed among five feature classes were calculated in all ROIs. Feature value differences between paired ROIs were evaluated using Bland-Altman 95% limits of agreement. For each feature, (1) the mean feature value change and (2) the difference between the upper and lower limits of agreement were normalized to the mean feature value to obtain, respectively, the normalized bias and normalized range of agreement (nRoA). Nonparametric tests were used to evaluate differences in normalized bias and nRoA across the three methods. Results: Because patient CT scans contained no pathology, minimal changes in feature values were expected (i.e., low nRoA and normalized bias). Seventy-five features with very large feature value variability (nRoA ≥ 100%) were excluded from further analysis. Across the remaining 65 features, significant differences in normalized bias were observed among the three methods. The lowest normalized bias (median: 0.06%) was achieved when feature values were calculated on original follow-up scans. The affine registration method

  1. Artificial feature-based multiview registration method for three-dimensional free-form object modeling

    NASA Astrophysics Data System (ADS)

    Ren, Tongqun; Zhu, Jigui; Guo, Yinbiao; Luo, Wei

    2010-05-01

    Two integral registration methods based on artificial features are described. In method one, independent global control points are designed to build a global coordinate system. Registration target and camera are also introduced to create intermediary coordinate systems. For each local scanning, one image of the whole measuring scene is shot by registration camera. Then local data can be unified to the global coordinate system by solving transition chains of various coordinate systems from this single image based on the projective geometry principle. In the other method, control points are placed on the object surface evenly and shot by registration camera from different positions and orientations. We solve their coordinates by employing the bundle adjustment method to build a global control network. The range sensor shoots at least three control points during each local scan. Then registration can be completed by mapping these control points into the global control network. In this work, the range sensor is untracked. Error accumulation and propagation are also effectively conquered, since overlapping of neighboring subregions is unessential. Experimental results are presented to show the feasibility of the proposed methods.

  2. The plant virus microscope image registration method based on mismatches removing.

    PubMed

    Wei, Lifang; Zhou, Shucheng; Dong, Heng; Mao, Qianzhuo; Lin, Jiaxiang; Chen, Riqing

    2016-01-01

    The electron microscopy is one of the major means to observe the virus. The view of virus microscope images is limited by making specimen and the size of the camera's view field. To solve this problem, the virus sample is produced into multi-slice for information fusion and image registration techniques are applied to obtain large field and whole sections. Image registration techniques have been developed in the past decades for increasing the camera's field of view. Nevertheless, these approaches typically work in batch mode and rely on motorized microscopes. Alternatively, the methods are conceived just to provide visually pleasant registration for high overlap ratio image sequence. This work presents a method for virus microscope image registration acquired with detailed visual information and subpixel accuracy, even when overlap ratio of image sequence is 10% or less. The method proposed focus on the correspondence set and interimage transformation. A mismatch removal strategy is proposed by the spatial consistency and the components of keypoint to enrich the correspondence set. And the translation model parameter as well as tonal inhomogeneities is corrected by the hierarchical estimation and model select. In the experiments performed, we tested different registration approaches and virus images, confirming that the translation model is not always stationary, despite the fact that the images of the sample come from the same sequence. The mismatch removal strategy makes building registration of virus microscope images at subpixel accuracy easier and optional parameters for building registration according to the hierarchical estimation and model select strategies make the proposed method high precision and reliable for low overlap ratio image sequence. PMID:26519816

  3. Affine Projection Algorithm with Improved Data-Selective Method Using the Condition Number

    NASA Astrophysics Data System (ADS)

    Ban, Sung Jun; Lee, Chang Woo; Kim, Sang Woo

    Recently, a data-selective method has been proposed to achieve low misalignment in affine projection algorithm (APA) by keeping the condition number of an input data matrix small. We present an improved method, and a complexity reduction algorithm for the APA with the data-selective method. Experimental results show that the proposed algorithm has lower misalignment and a lower condition number for an input data matrix than both the conventional APA and the APA with the previous data-selective method.

  4. Joint image registration and fusion method with a gradient strength regularization

    NASA Astrophysics Data System (ADS)

    Lidong, Huang; Wei, Zhao; Jun, Wang

    2015-05-01

    Image registration is an essential process for image fusion, and fusion performance can be used to evaluate registration accuracy. We propose a maximum likelihood (ML) approach to joint image registration and fusion instead of treating them as two independent processes in the conventional way. To improve the visual quality of a fused image, a gradient strength (GS) regularization is introduced in the cost function of ML. The GS of the fused image is controllable by setting the target GS value in the regularization term. This is useful because a larger target GS brings a clearer fused image and a smaller target GS makes the fused image smoother and thus restrains noise. Hence, the subjective quality of the fused image can be improved whether the source images are polluted by noise or not. We can obtain the fused image and registration parameters successively by minimizing the cost function using an iterative optimization method. Experimental results show that our method is effective with transformation, rotation, and scale parameters in the range of [-2.0, 2.0] pixel, [-1.1 deg, 1.1 deg], and [0.95, 1.05], respectively, and variances of noise smaller than 300. It also demonstrated that our method yields a more visual pleasing fused image and higher registration accuracy compared with a state-of-the-art algorithm.

  5. Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules IV: Electron-Propagator Methods.

    PubMed

    Dolgounitcheva, O; Díaz-Tinoco, Manuel; Zakrzewski, V G; Richard, Ryan M; Marom, Noa; Sherrill, C David; Ortiz, J V

    2016-02-01

    Comparison of ab initio electron-propagator predictions of vertical ionization potentials and electron affinities of organic, acceptor molecules with benchmark calculations based on the basis set-extrapolated, coupled cluster single, double, and perturbative triple substitution method has enabled identification of self-energy approximations with mean, unsigned errors between 0.1 and 0.2 eV. Among the self-energy approximations that neglect off-diagonal elements in the canonical, Hartree-Fock orbital basis, the P3 method for electron affinities, and the P3+ method for ionization potentials provide the best combination of accuracy and computational efficiency. For approximations that consider the full self-energy matrix, the NR2 methods offer the best performance. The P3+ and NR2 methods successfully identify the correct symmetry label of the lowest cationic state in two cases, naphthalenedione and benzoquinone, where some other methods fail. PMID:26730459

  6. A new affine-invariant image matching method based on SIFT

    NASA Astrophysics Data System (ADS)

    Wang, Peng-cheng; Chen, Qian; Chen, Hai-xin; Cheng, Hong-chang; Gong, Zhen-fei

    2013-09-01

    Local invariant feature extraction, as one of the main problems in the field of computer vision, has been widely applied to image matching, splicing and target recognition etc. Lowe's scale invariant feature transform (known as SIFT) algorithm has attracted much attention due to its invariance to scale, rotation and illumination. However, SIFT is not robust to affine deformations, because it is based on the DoG detector which extracts keypoints in a circle region. Besides, the feature descriptor is represented by a 128-dimensional vector, which means that the algorithm complexity is extremely large especially when there is a great quantity of keypoints in the image. In this paper, a new feature descriptor, which is robust to affine deformations, is proposed. Considering that circles turn to be ellipses after affine deformations, some improvements have been made. Firstly, the Gaussian image pyramids are constructed by convoluting the source image and the elliptical Gaussian kernel with two volatile parameters, orientation and eccentricity. In addition, the two parameters are discretely selected in order to imitate the possibilities of the affine deformation, which can make sure that anisotropic regions are transformed into isotropic ones. Next, all extreme points can be extracted as the candidates for the affine-invariant keypoints in the image pyramids. After accurate keypoints localization is performed, the secondary moment of the keypoints' neighborhood is calculated to identify the elliptical region which is affineinvariant, the same as SIFT, the main orientation of the keypoints can be determined and the feature descriptor is generated based on the histogram constructed in this region. At last, the PCA method for the 128-dimensional descriptor's reduction is used to improve the computer calculating efficiency. The experiments show that this new algorithm inherits all SIFT's original advantages, and has a good resistance to affine deformations; what's more, it

  7. Predicting the relative binding affinity of mineralocorticoid receptor antagonists by density functional methods.

    PubMed

    Roos, Katarina; Hogner, Anders; Ogg, Derek; Packer, Martin J; Hansson, Eva; Granberg, Kenneth L; Evertsson, Emma; Nordqvist, Anneli

    2015-12-01

    In drug discovery, prediction of binding affinity ahead of synthesis to aid compound prioritization is still hampered by the low throughput of the more accurate methods and the lack of general pertinence of one method that fits all systems. Here we show the applicability of a method based on density functional theory using core fragments and a protein model with only the first shell residues surrounding the core, to predict relative binding affinity of a matched series of mineralocorticoid receptor (MR) antagonists. Antagonists of MR are used for treatment of chronic heart failure and hypertension. Marketed MR antagonists, spironolactone and eplerenone, are also believed to be highly efficacious in treatment of chronic kidney disease in diabetes patients, but is contra-indicated due to the increased risk for hyperkalemia. These findings and a significant unmet medical need among patients with chronic kidney disease continues to stimulate efforts in the discovery of new MR antagonist with maintained efficacy but low or no risk for hyperkalemia. Applied on a matched series of MR antagonists the quantum mechanical based method gave an R(2) = 0.76 for the experimental lipophilic ligand efficiency versus relative predicted binding affinity calculated with the M06-2X functional in gas phase and an R(2) = 0.64 for experimental binding affinity versus relative predicted binding affinity calculated with the M06-2X functional including an implicit solvation model. The quantum mechanical approach using core fragments was compared to free energy perturbation calculations using the full sized compound structures. PMID:26572910

  8. A Comparison of Phase and Speckle Tracking Registration Methods for Motion Correction during HIFU Treatment

    NASA Astrophysics Data System (ADS)

    Yates, Tara; Smith, Penny Probert; Noble, Alison; Leslie, Tom; Kennedy, James

    2007-05-01

    The accuracy of treatment monitoring and planning is instrumental to the acceptance of HIFU surgery. The ability to locate, analyze and track a feature of interest during treatment will be affected by patient motion. Additionally, statistical analysis and temperature monitoring algorithms would benefit from the registration of successive frames. In this work two registration algorithms, which have had extensive trials in other imaging applications, are investigated. Their ability to reduce patient respiratory and cardiac motion is within ultrasound sequences, taken during HIFU treatments, is compared. The first algorithm is based on an intensity block matching approach with a similarity measure that incorporates speckle statistics explicitly. The second method registers phase representations of the image with a more general similarity measure. These methods would be expected to succeed on different aspects of the image: phase measurements give weight to features and are rotation and contrast invariant, whereas methods to track speckle are successful in images that lack strong features. In general phase based methods of registration are more robust and have the potential to be extended to multimodality registration (such as MRI to Ultrasound), however in this case tracking speckle may produce better results due to the low signal to noise ratio in ultrasound images taken during HIFU treatments. Numerous examples from HIFU surgery are presented to highlight the performance of each method under a various motion constraints. It is shown that the phase based algorithm is generally superior, except in the close proximity to the skin.

  9. Report: Affinity Chromatography.

    ERIC Educational Resources Information Center

    Walters, Rodney R.

    1985-01-01

    Supports, affinity ligands, immobilization, elution methods, and a number of applications are among the topics considered in this discussion of affinity chromatography. An outline of the basic principles of affinity chromatography is included. (JN)

  10. Evaluation of rigid registration methods for whole head imaging in diffuse optical tomography.

    PubMed

    Wu, Xue; Eggebrecht, Adam T; Ferradal, Silvina L; Culver, Joseph P; Dehghani, Hamid

    2015-07-01

    Functional brain imaging has become an important neuroimaging technique for the study of brain organization and development. Compared to other imaging techniques, diffuse optical tomography (DOT) is a portable and low-cost technique that can be applied to infants and hospitalized patients using an atlas-based light model. For DOT imaging, the accuracy of the forward model has a direct effect on the resulting recovered brain function within a field of view and so the accuracy of the spatially normalized atlas-based forward models must be evaluated. Herein, the accuracy of atlas-based DOT is evaluated on models that are spatially normalized via a number of different rigid registration methods on 24 subjects. A multileveled approach is developed to evaluate the correlation of the geometrical and sensitivity accuracies across the full field of view as well as within specific functional subregions. Results demonstrate that different registration methods are optimal for recovery of different sets of functional brain regions. However, the "nearest point to point" registration method, based on the EEG 19 landmark system, is shown to be the most appropriate registration method for image quality throughout the field of view of the high-density cap that covers the whole of the optically accessible cortex. PMID:26217675

  11. Automated registration of diagnostic to prediagnostic x-ray mammograms: Evaluation and comparison to radiologists' accuracy

    SciTech Connect

    Pinto Pereira, Snehal M.; Hipwell, John H.; McCormack, Valerie A.; Tanner, Christine; Moss, Sue M.; Wilkinson, Louise S.; Khoo, Lisanne A. L.; Pagliari, Catriona; Skippage, Pippa L.; Kliger, Carole J.; Hawkes, David J.; Santos Silva, Isabel M. dos

    2010-09-15

    Purpose: To compare and evaluate intensity-based registration methods for computation of serial x-ray mammogram correspondence. Methods: X-ray mammograms were simulated from MRIs of 20 women using finite element methods for modeling breast compressions and employing a MRI/x-ray appearance change model. The parameter configurations of three registration methods, affine, fluid, and free-form deformation (FFD), were optimized for registering x-ray mammograms on these simulated images. Five mammography film readers independently identified landmarks (tumor, nipple, and usually two other normal features) on pairs of diagnostic and corresponding prediagnostic digitized images from 52 breast cancer cases. Landmarks were independently reidentified by each reader. Target registration errors were calculated to compare the three registration methods using the reader landmarks as a gold standard. Data were analyzed using multilevel methods. Results: Between-reader variability varied with landmark (p<0.01) and screen (p=0.03), with between-reader mean distance (mm) in point location on the diagnostic/prediagnostic images of 2.50 (95% CI 1.95, 3.15)/2.84 (2.24, 3.55) for nipples and 4.26 (3.43, 5.24)/4.76 (3.85, 5.84) for tumors. Registration accuracy was sensitive to the type of landmark and the amount of breast density. For dense breasts ({>=}40%), the affine and fluid methods outperformed FFD. For breasts with lower density, the affine registration surpassed both fluid and FFD. Mean accuracy (mm) of the affine registration varied between 3.16 (95% CI 2.56, 3.90) for nipple points in breasts with density 20%-39% and 5.73 (4.80, 6.84) for tumor points in breasts with density <20%. Conclusions: Affine registration accuracy was comparable to that between independent film readers. More advanced two-dimensional nonrigid registration algorithms were incapable of increasing the accuracy of image alignment when compared to affine registration.

  12. Method for resurrecting negative electron affinity photocathodes after exposure to an oxidizing gas

    DOEpatents

    Mulhollan, Gregory A; Bierman, John C

    2012-10-30

    A method by which negative electron affinity photocathodes (201), single crystal, amorphous, or otherwise ordered, can be made to recover their quantum yield following exposure to an oxidizing gas has been discovered. Conventional recovery methods employ the use of cesium as a positive acting agent (104). In the improved recovery method, an electron beam (205), sufficiently energetic to generate a secondary electron cloud (207), is applied to the photocathode in need of recovery. The energetic beam, through the high secondary electron yield of the negative electron affinity surface (203), creates sufficient numbers of low energy electrons which act on the reduced-yield surface so as to negate the effects of absorbed oxidizing atoms thereby recovering the quantum yield to a pre-decay value.

  13. A Novel Open Tubular Capillary Electrochromatographic Method for Differentiating the DNA Interaction Affinity of Environmental Contaminants.

    PubMed

    D'Ulivo, Lucia; Feng, Yong-Lai

    2016-01-01

    The interaction of chemicals with DNA may lead to genotoxicity, mutation or carcinogenicity. A simple open tubular capillary electrochromatographic method is proposed to rapidly assess the interaction affinity of three environmental contaminants (1,4-phenylenediamine, pyridine and 2,4-diaminotoluene) to DNA by measuring their retention in the capillaries coated with DNA probes. DNA oligonucleotide probes were immobilized on the inner wall of a fused silica capillary that was first derivatized with 3-(aminopropyl)-triethoxysilane (APTES). The difference in retention times and factors was considered as the difference in interaction affinity of the contaminants to the DNA probes. The interaction of the contaminants with both double-stranded (dsDNA) and single-stranded DNA (ssDNA) coatings was compared. Retention factors of 1,4-phenylenediamine, pyridine and 2,4-diaminotoluene in the capillary coated with ssDNA probe were 0.29, 0.42, and 0.44, respectively. A similar trend was observed in the capillary coated with dsDNA, indicating that 2,4-diaminotoluene has the highest affinity among the three contaminants. The relative standard deviation (RSD) for the retention factors was in the range of 0.05-0.69% (n = 3). The results demonstrated that the developed technique could be applied for preliminary screening purpose to provide DNA interaction affinity information of various environmental contaminants. PMID:27055261

  14. A Novel Open Tubular Capillary Electrochromatographic Method for Differentiating the DNA Interaction Affinity of Environmental Contaminants

    PubMed Central

    D’Ulivo, Lucia; Feng, Yong-Lai

    2016-01-01

    The interaction of chemicals with DNA may lead to genotoxicity, mutation or carcinogenicity. A simple open tubular capillary electrochromatographic method is proposed to rapidly assess the interaction affinity of three environmental contaminants (1,4-phenylenediamine, pyridine and 2,4-diaminotoluene) to DNA by measuring their retention in the capillaries coated with DNA probes. DNA oligonucleotide probes were immobilized on the inner wall of a fused silica capillary that was first derivatized with 3-(aminopropyl)-triethoxysilane (APTES). The difference in retention times and factors was considered as the difference in interaction affinity of the contaminants to the DNA probes. The interaction of the contaminants with both double-stranded (dsDNA) and single-stranded DNA (ssDNA) coatings was compared. Retention factors of 1,4-phenylenediamine, pyridine and 2,4-diaminotoluene in the capillary coated with ssDNA probe were 0.29, 0.42, and 0.44, respectively. A similar trend was observed in the capillary coated with dsDNA, indicating that 2,4-diaminotoluene has the highest affinity among the three contaminants. The relative standard deviation (RSD) for the retention factors was in the range of 0.05–0.69% (n = 3). The results demonstrated that the developed technique could be applied for preliminary screening purpose to provide DNA interaction affinity information of various environmental contaminants. PMID:27055261

  15. Combining morphometric evidence from multiple registration methods using dempster-shafer theory

    NASA Astrophysics Data System (ADS)

    Rajagopalan, Vidya; Wyatt, Christopher

    2010-03-01

    In tensor-based morphometry (TBM) group-wise differences in brain structure are measured using high degreeof- freedom registration and some form of statistical test. However, it is known that TBM results are sensitive to both the registration method and statistical test used. Given the lack of an objective model of group variation is it difficult to determine a best registration method for TBM. The use of statistical tests is also problematic given the corrections required for multiple testing and the notorius difficulty selecting and intepreting signigance values. This paper presents an approach to address both of these issues by combining multiple registration methods using Dempster-Shafer Evidence theory to produce belief maps of categorical changes between groups. This approach is applied to the comparison brain morphometry in aging, a typical application of TBM, using the determinant of the Jacobian as a measure of volume change. We show that the Dempster-Shafer combination produces a unique and easy to interpret belief map of regional changes between and within groups without the complications associated with hypothesis testing.

  16. A MR-TRUS registration method for ultrasound-guided prostate interventions

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofeng; Rossi, Peter; Mao, Hui; Jani, Ashesh B.; Ogunleye, Tomi; Curran, Walter J.; Liu, Tian

    2015-03-01

    In this paper, we reported a MR-TRUS prostate registration method that uses a subject-specific prostate strain model to improve MR-targeted, US-guided prostate interventions (e.g., biopsy and radiotherapy). The proposed algorithm combines a subject-specific prostate strain model with a Bspline transformation to register the prostate gland of the MRI to the TRUS images. The prostate strain model was obtained through US elastography and a 3D strain map of the prostate was generated. The B-spline transformation was calculated by minimizing Euclidean distance between MR and TRUS prostate surfaces. This prostate stain map was used to constrain the B-spline-based transformation to predict and compensate for the internal prostate-gland deformation. This method was validated with a prostate-phantom experiment and a pilot study of 5 prostate-cancer patients. For the phantom study, the mean target registration error (TRE) was 1.3 mm. MR-TRUS registration was also successfully performed for 5 patients with a mean TRE less than 2 mm. The proposed registration method may provide an accurate and robust means of estimating internal prostate-gland deformation, and could be valuable for prostate-cancer diagnosis and treatment.

  17. Evaluation of optimization methods for intensity-based 2D-3D registration in x-ray guided interventions

    NASA Astrophysics Data System (ADS)

    van der Bom, I. M. J.; Klein, S.; Staring, M.; Homan, R.; Bartels, L. W.; Pluim, J. P. W.

    2011-03-01

    The advantage of 2D-3D image registration methods versus direct image-to-patient registration, is that these methods generally do not require user interaction (such as manual annotations), additional machinery or additional acquisition of 3D data. A variety of intensity-based similarity measures has been proposed and evaluated for different applications. These studies showed that the registration accuracy and capture range are influenced by the choice of similarity measure. However, the influence of the optimization method on intensity-based 2D-3D image registration has not been investigated. We have compared the registration performance of seven optimization methods in combination with three similarity measures: gradient difference, gradient correlation, and pattern intensity. Optimization methods included in this study were: regular step gradient descent, Nelder-Mead, Powell-Brent, Quasi-Newton, nonlinear conjugate gradient, simultaneous perturbation stochastic approximation, and evolution strategy. Registration experiments were performed on multiple patient data sets that were obtained during cerebral interventions. Various component combinations were evaluated on registration accuracy, capture range, and registration time. The results showed that for the same similarity measure, different registration accuracies and capture ranges were obtained when different optimization methods were used. For gradient difference, largest capture ranges were obtained with Powell-Brent and simultaneous perturbation stochastic approximation. Gradient correlation and pattern intensity had the largest capture ranges in combination with Powell-Brent, Nelder-Mead, nonlinear conjugate gradient, and Quasi-Newton. Average registration time, expressed in the number of DRRs required for convergence, was the lowest for Powell-Brent. Based on these results, we conclude that Powell-Brent is a reliable optimization method for intensity-based 2D-3D registration of x-ray images to CBCT

  18. A novel registration method for image-guided neurosurgery system based on stereo vision.

    PubMed

    An, Yong; Wang, Manning; Song, Zhijian

    2015-01-01

    This study presents a novel spatial registration method of Image-guided neurosurgery system (IGNS) based on stereo-vision. Images of the patient's head are captured by a video camera, which is calibrated and tracked by an optical tracking system. Then, a set of sparse facial data points are reconstructed from them by stereo vision in the patient space. Surface matching method is utilized to register the reconstructed sparse points and the facial surface reconstructed from preoperative images of the patient. Simulation experiments verified the feasibility of the proposed method. The proposed method it is a new low-cost and easy-to-use spatial registration method for IGNS, with good prospects for clinical application. PMID:26406100

  19. Using shape contexts method for registration of contra lateral breasts in thermal images

    PubMed Central

    Etehadtavakol, Mahnaz; Ng, Eddie Yin-Kwee; Gheissari, Niloofar

    2014-01-01

    AIM: To achieve symmetric boundaries for left and right breasts boundaries in thermal images by registration. METHODS: The proposed method for registration consists of two steps. In the first step, shape context, an approach as presented by Belongie and Malik was applied for registration of two breast boundaries. The shape context is an approach to measure shape similarity. Two sets of finite sample points from shape contours of two breasts are then presented. Consequently, the correspondences between the two shapes are found. By finding correspondences, the sample point which has the most similar shape context is obtained. RESULTS: In this study, a line up transformation which maps one shape onto the other has been estimated in order to complete shape. The used of a thin plate spline permitted good estimation of a plane transformation which has capability to map unselective points from one shape onto the other. The obtained aligning transformation of boundaries points has been applied successfully to map the two breasts interior points. Some of advantages for using shape context method in this work are as follows: (1) no special land marks or key points are needed; (2) it is tolerant to all common shape deformation; and (3) although it is uncomplicated and straightforward to use, it gives remarkably powerful descriptor for point sets significantly upgrading point set registration. Results are very promising. The proposed algorithm was implemented for 32 cases. Boundary registration is done perfectly for 28 cases. CONCLUSION: We used shape contexts method that is simple and easy to implement to achieve symmetric boundaries for left and right breasts boundaries in thermal images. PMID:25493241

  20. A 3D neurovascular bundles segmentation method based on MR-TRUS deformable registration

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofeng; Rossi, Peter; Jani, Ashesh B.; Mao, Hui; Ogunleye, Tomi; Curran, Walter J.; Liu, Tian

    2015-03-01

    In this paper, we propose a 3D neurovascular bundles (NVB) segmentation method for ultrasound (US) image by integrating MR and transrectal ultrasound (TRUS) images through MR-TRUS deformable registration. First, 3D NVB was contoured by a physician in MR images, and the 3D MRdefined NVB was then transformed into US images using a MR-TRUS registration method, which models the prostate tissue as an elastic material, and jointly estimates the boundary deformation and the volumetric deformations under the elastic constraint. This technique was validated with a clinical study of 6 patients undergoing radiation therapy (RT) treatment for prostate cancer. The accuracy of our approach was assessed through the locations of landmarks, as well as previous ultrasound Doppler images of patients. MR-TRUS registration was successfully performed for all patients. The mean displacement of the landmarks between the post-registration MR and TRUS images was less than 2 mm, and the average NVB volume Dice Overlap Coefficient was over 89%. This NVB segmentation technique could be a useful tool as we try to spare the NVB in prostate RT, monitor NVB response to RT, and potentially improve post-RT potency outcomes.

  1. Device and methods for "gold standard" registration of clinical 3D and 2D cerebral angiograms

    NASA Astrophysics Data System (ADS)

    Madan, Hennadii; Likar, Boštjan; Pernuš, Franjo; Å piclin, Žiga

    2015-03-01

    Translation of any novel and existing 3D-2D image registration methods into clinical image-guidance systems is limited due to lack of their objective validation on clinical image datasets. The main reason is that, besides the calibration of the 2D imaging system, a reference or "gold standard" registration is very difficult to obtain on clinical image datasets. In the context of cerebral endovascular image-guided interventions (EIGIs), we present a calibration device in the form of a headband with integrated fiducial markers and, secondly, propose an automated pipeline comprising 3D and 2D image processing, analysis and annotation steps, the result of which is a retrospective calibration of the 2D imaging system and an optimal, i.e., "gold standard" registration of 3D and 2D images. The device and methods were used to create the "gold standard" on 15 datasets of 3D and 2D cerebral angiograms, whereas each dataset was acquired on a patient undergoing EIGI for either aneurysm coiling or embolization of arteriovenous malformation. The use of the device integrated seamlessly in the clinical workflow of EIGI. While the automated pipeline eliminated all manual input or interactive image processing, analysis or annotation. In this way, the time to obtain the "gold standard" was reduced from 30 to less than one minute and the "gold standard" of 3D-2D registration on all 15 datasets of cerebral angiograms was obtained with a sub-0.1 mm accuracy.

  2. A method to estimate the effect of deformable image registration uncertainties on daily dose mapping

    SciTech Connect

    Murphy, Martin J.; Salguero, Francisco J.; Siebers, Jeffrey V.; Staub, David; Vaman, Constantin

    2012-02-15

    Purpose: To develop a statistical sampling procedure for spatially-correlated uncertainties in deformable image registration and then use it to demonstrate their effect on daily dose mapping. Methods: Sequential daily CT studies are acquired to map anatomical variations prior to fractionated external beam radiotherapy. The CTs are deformably registered to the planning CT to obtain displacement vector fields (DVFs). The DVFs are used to accumulate the dose delivered each day onto the planning CT. Each DVF has spatially-correlated uncertainties associated with it. Principal components analysis (PCA) is applied to measured DVF error maps to produce decorrelated principal component modes of the errors. The modes are sampled independently and reconstructed to produce synthetic registration error maps. The synthetic error maps are convolved with dose mapped via deformable registration to model the resulting uncertainty in the dose mapping. The results are compared to the dose mapping uncertainty that would result from uncorrelated DVF errors that vary randomly from voxel to voxel. Results: The error sampling method is shown to produce synthetic DVF error maps that are statistically indistinguishable from the observed error maps. Spatially-correlated DVF uncertainties modeled by our procedure produce patterns of dose mapping error that are different from that due to randomly distributed uncertainties. Conclusions: Deformable image registration uncertainties have complex spatial distributions. The authors have developed and tested a method to decorrelate the spatial uncertainties and make statistical samples of highly correlated error maps. The sample error maps can be used to investigate the effect of DVF uncertainties on daily dose mapping via deformable image registration. An initial demonstration of this methodology shows that dose mapping uncertainties can be sensitive to spatial patterns in the DVF uncertainties.

  3. Seed-based transrectal ultrasound-fluoroscopy registration method for intraoperative dosimetry analysis of prostate brachytherapy

    SciTech Connect

    Tutar, Ismail B.; Gong Lixin; Narayanan, Sreeram; Pathak, Sayan D.; Cho, Paul S.; Wallner, Kent; Kim, Yongmin

    2008-03-15

    Prostate brachytherapy is an effective treatment option for early-stage prostate cancer. During a prostate brachytherapy procedure, transrectal ultrasound (TRUS) and fluoroscopy imaging modalities complement each other by providing good visualization of soft tissue and implanted seeds, respectively. Therefore, the registration of these two imaging modalities, which are readily available in the operating room, could facilitate intraoperative dosimetry, thus enabling physicians to implant additional seeds into the underdosed portions of the prostate while the patient is still on the operating table. It is desirable to register TRUS and fluoroscopy images by using the seeds as fiducial markers. Although the locations of all the implanted seeds can be reconstructed from three fluoroscopy images, only a fraction of these seeds can be located in TRUS images. It is challenging to register the TRUS and fluoroscopy images by using the identified seeds, since the correspondence between them is unknown. Furthermore, misdetection of nonseed structures as seeds can lead to the inclusion of spurious points in the data set. We developed a new method called iterative optimal assignment (IOA) to overcome these challenges in TRUS-fluoroscopy registration. By using the Hungarian method in an optimization framework, IOA computes a set of transformation parameters that yield the one-to-one correspondence with minimum cost. We have evaluated our registration method at varying noise levels, seed detection rates, and number of spurious points using data collected from 25 patients. We have found that IOA can perform registration with an average root mean square error of about 0.2 cm even when the seed detection rate is only 10%. We believe that IOA can offer a robust solution to seed-based TRUS-fluoroscopy registration, thus making intraoperative dosimetry possible.

  4. Comparison of landmark-based and automatic methods for cortical surface registration.

    PubMed

    Pantazis, Dimitrios; Joshi, Anand; Jiang, Jintao; Shattuck, David W; Bernstein, Lynne E; Damasio, Hanna; Leahy, Richard M

    2010-02-01

    Group analysis of structure or function in cerebral cortex typically involves, as a first step, the alignment of cortices. A surface-based approach to this problem treats the cortex as a convoluted surface and coregisters across subjects so that cortical landmarks or features are aligned. This registration can be performed using curves representing sulcal fundi and gyral crowns to constrain the mapping. Alternatively, registration can be based on the alignment of curvature metrics computed over the entire cortical surface. The former approach typically involves some degree of user interaction in defining the sulcal and gyral landmarks while the latter methods can be completely automated. Here we introduce a cortical delineation protocol consisting of 26 consistent landmarks spanning the entire cortical surface. We then compare the performance of a landmark-based registration method that uses this protocol with that of two automatic methods implemented in the software packages FreeSurfer and BrainVoyager. We compare performance in terms of discrepancy maps between the different methods, the accuracy with which regions of interest are aligned, and the ability of the automated methods to correctly align standard cortical landmarks. Our results show similar performance for ROIs in the perisylvian region for the landmark-based method and FreeSurfer. However, the discrepancy maps showed larger variability between methods in occipital and frontal cortex and automated methods often produce misalignment of standard cortical landmarks. Consequently, selection of the registration approach should consider the importance of accurate sulcal alignment for the specific task for which coregistration is being performed. When automatic methods are used, the users should ensure that sulci in regions of interest in their studies are adequately aligned before proceeding with subsequent analysis. PMID:19796696

  5. Assessment of Thematic Mapper Band-to-band Registration by the Block Correlation Method

    NASA Technical Reports Server (NTRS)

    Card, D. H.; Wrigley, R. C.; Mertz, F. C.; Hall, J. R.

    1984-01-01

    The design of the Thematic Mapper (TM) multispectral radiometer makes it susceptible to band-to-band misregistration. To estimate band-to-band misregistration a block correlation method is employed. This method is chosen over other possible techniques (band differencing and flickering) because quantitative results are produced. The method correlates rectangular blocks of pixels from one band against blocks centered on identical pixels from a second band. The block pairs are shifted in pixel increments both vertically and horizontally with respect to each other and the correlation coefficient for each shift position is computed. The displacement corresponding to the maximum correlation is taken as the best estimate of registration error for each block pair. Subpixel shifts are estimated by a bi-quadratic interpolation of the correlation values surrounding the maximum correlation. To obtain statistical summaries for each band combination post processing of the block correlation results performed. The method results in estimates of registration error that are consistent with expectations.

  6. Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method

    PubMed Central

    Muddana, Hari S.; Yin, Jian; Sapra, Neil V.; Fenley, Andrew T.; Gilson, Michael K.

    2014-01-01

    Accurate methods for predicting protein-ligand binding affinities are of central interest to computer-aided drug design for hit identification and lead optimization. Here, we used the mining minima (M2) method to predict cucurbit[7]uril binding affinities from the SAMPL4 blind prediction challenge. We tested two different energy models, an empirical classical force field, CHARMm with VCharge charges, and the Poisson-Boltzmann Surface Area (PBSA) solvation model; and a semiempirical quantum mechanical Hamiltonian, PM6-DH+, coupled with the COSMO solvation model and a surface area term for nonpolar solvation free energy. Binding affinities based on the classical force field correlated strongly with the experiments with a correlation coefficient (R2) of 0.74. On the other hand, binding affinities based on the quantum mechanical energy model correlated poorly with experiments (R2 = 0.24), due largely to two major outliers. As we used extensive conformational search methods, these results point to possible inaccuracies in the PM6-DH+ energy model or the COSMO solvation model. Furthermore, the different binding free energy components, solute energy, solvation free energy, and configurational entropy showed significant deviations between the classical M2 and quantum M2 calculations. Comparison of different classical M2 free energy components to experiments show that the change in the total energy, i.e. the solute energy plus the solvation free energy, is the key driving force for binding, with a reasonable correlation to experiment (R2 = 0.56); however, accounting for configurational entropy further improves the correlation. PMID:24510191

  7. Method for trapping affinity chromatography of transcription factors using aldehyde-hydrazide coupling to agarose.

    PubMed

    Jia, Yinshan; Jarrett, Harry W

    2015-08-01

    The use of a method of coupling DNA was investigated for trapping and purifying transcription factors. Using the GFP-C/EBP (CAAT/enhancer binding protein) fusion protein as a model, trapping gives higher purity and comparable yield to conventional affinity chromatography. The chemistry used is mild and was shown to have no detrimental effect on GFP fluorescence or GFP-C/EBP DNA binding. The method involves introducing a ribose nucleotide to the 3' end of a DNA sequence. Reaction with mM NaIO4 (sodium metaperiodate) produces a dialdehyde of ribose that couples to hydrazide-agarose. The DNA is combined at nM concentration with a nuclear extract or other protein mixture, and DNA-protein complexes form. The complex is then coupled to hydrazide-agarose for trapping the DNA-protein complex and the protein eluted by increasing NaCl concentration. Using a different oligonucleotide with the proximal E-box sequence from the human telomerase promoter, USF-2 transcription factor was purified by trapping, again with higher purity than results from conventional affinity chromatography and similar yield. Other transcription factors binding E-boxes, including E2A, c-Myc, and Myo-D, were also purified, but myogenin and NFκB were not. Therefore, this approach proved to be valuable for both affinity chromatography and the trapping approach. PMID:25935261

  8. Method for trapping affinity chromatography of transcription factors using aldehyde-hydrazide coupling to agarose

    PubMed Central

    Jia, Yinshan; Jarrett, Harry W.

    2015-01-01

    The uses of a method of coupling DNA is investigated for trapping and purifying transcription factors. Using the GFP-C/EBP fusion protein as a model, trapping gives higher purity and comparable yield to conventional affinity chromatography. The chemistry utilized is mild and was shown to have no detrimental effect on GFP fluorescence or GFP-C/EBP DNA-binding. The method involves introducing a ribose nucleotide to the 3′ end of a DNA sequence. Reaction with mM NaIO4 (sodium metaperiodate) produces a dialdehyde of ribose which couples to hydrazide-agarose. The DNA is combined at nM concentration with a nuclear extract or other protein mixture and DNA-protein complexes form. The complex is then coupled to hydrazide-agarose for trapping the DNA-protein complex and the protein eluted by increasing NaCl concentration. Using a different oligonucleotide with the proximal E-box sequence from the human telomerase promoter, USF-2 transcription factor was purified by trapping, again with higher purity than results from conventional affinity chromatography and similar yield. Other transcription factors binding E-boxes including E2A, c-myc, and myo-D were also purified but myogenenin and NFκB were not. Therfore, this approach proved valuable for both affinity chromatography and for the trapping approach. PMID:25935261

  9. A fast inverse consistent deformable image registration method based on symmetric optical flow computation

    PubMed Central

    Li, Hua; Low, Daniel A; Deasy, Joseph O; Naqa, Issam El

    2014-01-01

    Deformable image registration is widely used in various radiation therapy applications including daily treatment planning adaptation to map planned tissue or dose to changing anatomy. In this work, a simple and efficient inverse consistency deformable registration method is proposed with aims of higher registration accuracy and faster convergence speed. Instead of registering image I to a second image J, the two images are symmetrically deformed toward one another in multiple passes, until both deformed images are matched and correct registration is therefore achieved. In each pass, a delta motion field is computed by minimizing a symmetric optical flow system cost function using modified optical flow algorithms. The images are then further deformed with the delta motion field in the positive and negative directions respectively, and then used for the next pass. The magnitude of the delta motion field is forced to be less than 0.4 voxel for every pass in order to guarantee smoothness and invertibility for the two overall motion fields that are accumulating the delta motion fields in both positive and negative directions, respectively. The final motion fields to register the original images I and J, in either direction, are calculated by inverting one overall motion field and combining the inversion result with the other overall motion field. The final motion fields are inversely consistent and this is ensured by the symmetric way that registration is carried out. The proposed method is demonstrated with phantom images, artificially deformed patient images and 4D-CT images. Our results suggest that the proposed method is able to improve the overall accuracy (reducing registration error by 30% or more, compared to the original and inversely inconsistent optical flow algorithms), reduce the inverse consistency error (by 95% or more) and increase the convergence rate (by 100% or more). The overall computation speed may slightly decrease, or increase in most cases

  10. A liver registration method for segmented multi-phase CT images

    NASA Astrophysics Data System (ADS)

    Shi, Shuyue; Yuan, Rong; Sun, Zhi; Xie, Qingguo

    2015-03-01

    In order to build high quality geometric models for liver containing vascular system, multi-phase CT series used in a computer-aided diagnosis and surgical planning system aims at liver diseases have to be accurately registered. In this paper we model the segmented liver containing vascular system as a complex shape and propose a two-step registration method. Without any tree modeling for vessel this method can carry out a simultaneous registration for both liver tissue and vascular system inside. Firstly a rigid aligning using vessel as feature is applied on the complex shape model while genetic algorithm is used as the optimization method. Secondly we achieve the elastic shape registration by combine the incremental free form deformation (IFFD) with a modified iterative closest point (ICP) algorithm. Inspired by the concept of demons method, we propose to calculate a fastest diffusion vector (FDV) for each control point on the IFFD lattice to replace the points correspondence needed in ICP iterations. Under the iterative framework of the modified ICP, the optimal solution of control points' displacement in every IFFD level can be obtained efficiently. The method has been quantitatively evaluated on clinical multi-phase CT series.

  11. A Log-Euclidean polyaffine registration for articulated structures in medical images.

    PubMed

    Martín-Fernández, Miguel Angel; Martín-Fernández, Marcos; Alberola-López, Carlos

    2009-01-01

    In this paper we generalize the Log-Euclidean polyaffine registration framework of Arsigny et al. to deal with articulated structures. This framework has very useful properties as it guarantees the invertibility of smooth geometric transformations. In articulated registration a skeleton model is defined for rigid structures such as bones. The final transformation is affine for the bones and elastic for other tissues in the image. We extend the Arsigny el al.'s method to deal with locally-affine registration of pairs of wires. This enables the possibility of using this registration framework to deal with articulated structures. In this context, the design of the weighting functions, which merge the affine transformations defined for each pair of wires, has a great impact not only on the final result of the registration algorithm, but also on the invertibility of the global elastic transformation. Several experiments, using both synthetic images and hand radiographs, are also presented. PMID:20425983

  12. Evaluation of deformable image registration methods for dose monitoring in head and neck radiotherapy.

    PubMed

    Rigaud, Bastien; Simon, Antoine; Castelli, Joël; Gobeli, Maxime; Ospina Arango, Juan-David; Cazoulat, Guillaume; Henry, Olivier; Haigron, Pascal; De Crevoisier, Renaud

    2015-01-01

    In the context of head and neck cancer (HNC) adaptive radiation therapy (ART), the two purposes of the study were to compare the performance of multiple deformable image registration (DIR) methods and to quantify their impact for dose accumulation, in healthy structures. Fifteen HNC patients had a planning computed tomography (CT0) and weekly CTs during the 7 weeks of intensity-modulated radiation therapy (IMRT). Ten DIR approaches using different registration methods (demons or B-spline free form deformation (FFD)), preprocessing, and similarity metrics were tested. Two observers identified 14 landmarks (LM) on each CT-scan to compute LM registration error. The cumulated doses estimated by each method were compared. The two most effective DIR methods were the demons and the FFD, with both the mutual information (MI) metric and the filtered CTs. The corresponding LM registration accuracy (precision) was 2.44 mm (1.30 mm) and 2.54 mm (1.33 mm), respectively. The corresponding LM estimated cumulated dose accuracy (dose precision) was 0.85 Gy (0.93 Gy) and 0.88 Gy (0.95 Gy), respectively. The mean uncertainty (difference between maximal and minimal dose considering all the 10 methods) to estimate the cumulated mean dose to the parotid gland (PG) was 4.03 Gy (SD = 2.27 Gy, range: 1.06-8.91 Gy). PMID:25759821

  13. A Comparative Study of Registration Methods for RGB-D Video of Static Scenes

    PubMed Central

    Morell-Gimenez, Vicente; Saval-Calvo, Marcelo; Azorin-Lopez, Jorge; Garcia-Rodriguez, Jose; Cazorla, Miguel; Orts-Escolano, Sergio; Fuster-Guillo, Andres

    2014-01-01

    The use of RGB-D sensors for mapping and recognition tasks in robotics or, in general, for virtual reconstruction has increased in recent years. The key aspect of these kinds of sensors is that they provide both depth and color information using the same device. In this paper, we present a comparative analysis of the most important methods used in the literature for the registration of subsequent RGB-D video frames in static scenarios. The analysis begins by explaining the characteristics of the registration problem, dividing it into two representative applications: scene modeling and object reconstruction. Then, a detailed experimentation is carried out to determine the behavior of the different methods depending on the application. For both applications, we used standard datasets and a new one built for object reconstruction. PMID:24834909

  14. Comparison and evaluation of joint histogram estimation methods for mutual information based image registration

    NASA Astrophysics Data System (ADS)

    Liang, Yongfang; Chen, Hua-mei

    2005-04-01

    Joint histogram is the only quantity required to calculate the mutual information (MI) between two images. For MI based image registration, joint histograms are often estimated through linear interpolation or partial volume interpolation (PVI). It has been pointed out that both methods may result in a phenomenon known as interpolation induced artifacts. In this paper, we implemented a wide range of interpolation/approximation kernels for joint histogram estimation. Some kernels are nonnegative. In this case, these kernels are applied in two ways as the linear kernel is applied in linear interpolation and PVI. In addition, we implemented two other joint histogram estimation methods devised to overcome the interpolation artifact problem. They are nearest neighbor interpolation with jittered sampling with/without histogram blurring and data resampling. We used the clinical data obtained from Vanderbilt University for all of the experiments. The objective of this study is to perform a comprehensive comparison and evaluation of different joint histogram estimation methods for MI based image registration in terms of artifacts reduction and registration accuracy.

  15. Scope and applications of translation invariant wavelets to image registration

    NASA Technical Reports Server (NTRS)

    Chettri, Samir; LeMoigne, Jacqueline; Campbell, William

    1997-01-01

    The first part of this article introduces the notion of translation invariance in wavelets and discusses several wavelets that have this property. The second part discusses the possible applications of such wavelets to image registration. In the case of registration of affinely transformed images, we would conclude that the notion of translation invariance is not really necessary. What is needed is affine invariance and one way to do this is via the method of moment invariants. Wavelets or, in general, pyramid processing can then be combined with the method of moment invariants to reduce the computational load.

  16. Methylsorb: a simple method for quantifying DNA methylation using DNA-gold affinity interactions.

    PubMed

    Sina, Abu Ali Ibn; Carrascosa, Laura G; Palanisamy, Ramkumar; Rauf, Sakandar; Shiddiky, Muhammad J A; Trau, Matt

    2014-10-21

    The analysis of DNA methylation is becoming increasingly important both in the clinic and also as a research tool to unravel key epigenetic molecular mechanisms in biology. Current methodologies for the quantification of regional DNA methylation (i.e., the average methylation over a region of DNA in the genome) are largely affected by comprehensive DNA sequencing methodologies which tend to be expensive, tedious, and time-consuming for many applications. Herein, we report an alternative DNA methylation detection method referred to as "Methylsorb", which is based on the inherent affinity of DNA bases to the gold surface (i.e., the trend of the affinity interactions is adenine > cytosine ≥ guanine > thymine).1 Since the degree of gold-DNA affinity interaction is highly sequence dependent, it provides a new capability to detect DNA methylation by simply monitoring the relative adsorption of bisulfite treated DNA sequences onto a gold chip. Because the selective physical adsorption of DNA fragments to gold enable a direct read-out of regional DNA methylation, the current requirement for DNA sequencing is obviated. To demonstrate the utility of this method, we present data on the regional methylation status of two CpG clusters located in the EN1 and MIR200B genes in MCF7 and MDA-MB-231 cells. The methylation status of these regions was obtained from the change in relative mass on gold surface with respect to relative adsorption of an unmethylated DNA source and this was detected using surface plasmon resonance (SPR) in a label-free and real-time manner. We anticipate that the simplicity of this method, combined with the high level of accuracy for identifying the methylation status of cytosines in DNA, could find broad application in biology and diagnostics. PMID:25226077

  17. Automatic and robust method for registration of optical imagery with point cloud data

    NASA Astrophysics Data System (ADS)

    Wu, Yingdan; Ming, Yang

    2015-12-01

    Aim to the difficulty of automatic and robust registration of optical imagery with point cloud data, this paper propose a new method based on SIFT and Mutual Information (MI). The SIFT features are firstly extracted and matched, whose result is used to derive the coarse geometric relationship between the optical imagery and the point cloud data. Secondly, the MI-based similarity measure is used to derive the conjugate points. And then the RANSAC algorithm is adopted to eliminate the erroneous matching points. Repeating the procedure of MI matching and mismatching points deletion until the finest pyramid image level. Using the matching results, the transform model is determined. The experiments have been made and they demonstrate the potential of the MI-based measure for the registration of optical imagery with the point cloud data, and this highlight the feasibility and robustness of the method proposed in this paper to automated registration of multi-modal, multi-temporal remote sensing data for a wide range of applications.

  18. Text messaging as a new method for injury registration in sports: a methodological study in elite female football.

    PubMed

    Nilstad, A; Bahr, R; Andersen, T E

    2014-02-01

    Methodological differences in epidemiologic studies have led to significant discrepancies in injury incidences reported. The aim of this study was to evaluate text messaging as a new method for injury registration in elite female football players and to compare this method with routine medical staff registration. Twelve teams comprising 228 players prospectively recorded injuries and exposure through one competitive football season. Players reported individually by answering three text messages once a week. A designated member of the medical staff conducted concurrent registrations of injuries and exposure. Injuries and exposure were compared between medical staff registrations from nine teams and their 159 affiliated players. During the football season, a total of 232 time-loss injuries were recorded. Of these, 62% were captured through individual registration only, 10% by the medical staff only, and 28% were reported through both methods. The incidence of training injuries was 3.7 per 1000 player hours when calculated from individual registration vs 2.2 from medical staff registration [rate ratio (RR): 1.7, 1.2-2.4]. For match injuries, the corresponding incidences were 18.6 vs 5.4 (RR: 3.4, 2.4-4.9), respectively. There was moderate agreement for severity classifications in injury cases reported by both methods (kappa correlation coefficient: 0.48, confidence interval: 0.30-0.66). PMID:22537065

  19. A contrast correction method for dental images based on histogram registration

    PubMed Central

    Economopoulos, TL; Asvestas, PA; Matsopoulos, GK; Gröndahl, K; Gröndahl, H-G

    2010-01-01

    Contrast correction is often required in digital subtraction radiography when comparing medical data acquired over different time periods owing to dissimilarities in the acquisition process. This paper focuses on dental radiographs and introduces a novel approach for correcting the contrast in dental image pairs. The proposed method modifies the subject images by applying typical registration techniques on their histograms. The proposed histogram registration method reshapes the histograms of the two subject images in such a way that these images are matched in terms of their contrast deviation. The method was extensively tested over 4 sets of dental images, consisting of 72 registered dental image pairs with unknown contrast differences as well as 20 dental pairs with known contrast differences. The proposed method was directly compared against the well-known histogram-based contrast correction method. The two methods were qualitatively and quantitatively evaluated for all 92 available dental image pairs. The two methods were compared in terms of the contrast root mean square difference between the reference image and the corrected image in each case. The obtained results were also verified statistically using appropriate t-tests in each set. The proposed method exhibited superior performance compared with the well-established method, in terms of the contrast root mean square difference between the reference and the corrected images. After suitable statistical analysis, it was deduced that the performance advantage of the proposed approach was statistically significant. PMID:20587655

  20. An enhanced method for registration of dental surfaces partially scanned by a 3D dental laser scanning.

    PubMed

    Park, Seongjin; Kang, Ho Chul; Lee, Jeongjin; Shin, Juneseuk; Shin, Yeong Gil

    2015-01-01

    In this paper, we propose the fast and accurate registration method of partially scanned dental surfaces in a 3D dental laser scanning. To overcome the multiple point correspondence problems of conventional surface registration methods, we propose the novel depth map-based registration method to register 3D surface models. First, we convert a partially scanned 3D dental surface into a 2D image by generating the 2D depth map image of the surface model by applying a 3D rigid transformation into this model. Then, the image-based registration method using 2D depth map images accurately estimates the initial transformation between two consequently acquired surface models. To further increase the computational efficiency, we decompose the 3D rigid transformation into out-of-plane (i.e. x-, y-rotation, and z-translation) and in-plane (i.e. x-, y-translation, and z-rotation) transformations. For the in-plane transformation, we accelerate the transformation process by transforming the 2D depth map image instead of transforming the 3D surface model. For the more accurate registration of 3D surface models, we enhance iterative closest point (ICP) method for the subsequent fine registration. Our initial depth map-based registration well aligns each surface model. Therefore, our subsequent ICP method can accurately register two surface models since it is highly probable that the closest point pairs are the exact corresponding point pairs. The experimental results demonstrated that our method accurately registered partially scanned dental surfaces. Regarding the computational performance, our method delivered about 1.5 times faster registration than the conventional method. Our method can be successfully applied to the accurate reconstruction of 3D dental objects for orthodontic and prosthodontic treatment. PMID:25453381

  1. The tandem affinity purification method: an efficient system for protein complex purification and protein interaction identification.

    PubMed

    Xu, Xiaoli; Song, Yuan; Li, Yuhua; Chang, Jianfeng; Zhang, Hua; An, Lizhe

    2010-08-01

    Isolation and identification of protein partners in multi-protein complexes are important in gaining further insights into the cellular roles of proteins and determining the possible mechanisms by which proteins have an effect in the molecular environment. The tandem affinity purification (TAP) method was originally developed in yeast for the purification of protein complexes and identification of protein-protein interactions. With modifications to this method and many variations in the original tag made over the past few years, the TAP system could be applied in mammalian, plant, bacteria and other systems for protein complex analysis. In this review, we describe the application of the TAP method in various organisms, the modification in the tag, the disadvantages, the developments and the future prospects of the TAP method. PMID:20399864

  2. An adaptive MR-CT registration method for MRI-guided prostate cancer radiotherapy

    NASA Astrophysics Data System (ADS)

    Zhong, Hualiang; Wen, Ning; Gordon, James J.; Elshaikh, Mohamed A.; Movsas, Benjamin; Chetty, Indrin J.

    2015-04-01

    Magnetic Resonance images (MRI) have superior soft tissue contrast compared with CT images. Therefore, MRI might be a better imaging modality to differentiate the prostate from surrounding normal organs. Methods to accurately register MRI to simulation CT images are essential, as we transition the use of MRI into the routine clinic setting. In this study, we present a finite element method (FEM) to improve the performance of a commercially available, B-spline-based registration algorithm in the prostate region. Specifically, prostate contours were delineated independently on ten MRI and CT images using the Eclipse treatment planning system. Each pair of MRI and CT images was registered with the B-spline-based algorithm implemented in the VelocityAI system. A bounding box that contains the prostate volume in the CT image was selected and partitioned into a tetrahedral mesh. An adaptive finite element method was then developed to adjust the displacement vector fields (DVFs) of the B-spline-based registrations within the box. The B-spline and FEM-based registrations were evaluated based on the variations of prostate volume and tumor centroid, the unbalanced energy of the generated DVFs, and the clarity of the reconstructed anatomical structures. The results showed that the volumes of the prostate contours warped with the B-spline-based DVFs changed 10.2% on average, relative to the volumes of the prostate contours on the original MR images. This discrepancy was reduced to 1.5% for the FEM-based DVFs. The average unbalanced energy was 2.65 and 0.38 mJ cm-3, and the prostate centroid deviation was 0.37 and 0.28 cm, for the B-spline and FEM-based registrations, respectively. Different from the B-spline-warped MR images, the FEM-warped MR images have clear boundaries between prostates and bladders, and their internal prostatic structures are consistent with those of the original MR images. In summary, the developed adaptive FEM method preserves the prostate volume

  3. Improving an affine and non-linear image registration and/or segmentation task by incorporating characteristics of the displacement field

    NASA Astrophysics Data System (ADS)

    Ens, Konstantin; Heldmann, Stefan; Modersitzki, Jan; Fischer, Bernd

    2009-02-01

    Image registration is an important and active area of medical image processing. Given two images, the idea is to compute a reasonable displacement field which deforms one image such that it becomes similar to the other image. The design of an automatic registration scheme is a tricky task and often the computed displacement field has to be discarded, when the outcome is not satisfactory. On the other hand, however, any displacement field does contain useful information on the underlying images. It is the idea of this note, to utilize this information and to benefit from an even unsuccessful attempt for the subsequent treatment of the images. Here, we make use of typical vector analysis operators like the divergence and curl operator to identify meaningful portions of the displacement field to be used in a follow-up run. The idea is illustrated with the help of academic as well as a real life medical example. It is demonstrated on how the novel methodology may be used to substantially improve a registration result and to solve a difficult segmentation problem.

  4. Graphlet signature-based scoring method to estimate protein–ligand binding affinity

    PubMed Central

    Singh, Omkar; Sawariya, Kunal; Aparoy, Polamarasetty

    2014-01-01

    Over the years, various computational methodologies have been developed to understand and quantify receptor–ligand interactions. Protein–ligand interactions can also be explained in the form of a network and its properties. The ligand binding at the protein-active site is stabilized by formation of new interactions like hydrogen bond, hydrophobic and ionic. These non-covalent interactions when considered as links cause non-isomorphic sub-graphs in the residue interaction network. This study aims to investigate the relationship between these induced sub-graphs and ligand activity. Graphlet signature-based analysis of networks has been applied in various biological problems; the focus of this work is to analyse protein–ligand interactions in terms of neighbourhood connectivity and to develop a method in which the information from residue interaction networks, i.e. graphlet signatures, can be applied to quantify ligand affinity. A scoring method was developed, which depicts the variability in signatures adopted by different amino acids during inhibitor binding, and was termed as GSUS (graphlet signature uniqueness score). The score is specific for every individual inhibitor. Two well-known drug targets, COX-2 and CA-II and their inhibitors, were considered to assess the method. Residue interaction networks of COX-2 and CA-II with their respective inhibitors were used. Only hydrogen bond network was considered to calculate GSUS and quantify protein–ligand interaction in terms of graphlet signatures. The correlation of the GSUS with pIC50 was consistent in both proteins and better in comparison to the Autodock results. The GSUS scoring method was better in activity prediction of molecules with similar structure and diverse activity and vice versa. This study can be a major platform in developing approaches that can be used alone or together with existing methods to predict ligand affinity from protein–ligand complexes. PMID:26064572

  5. Sandwich fluorimetric method for specific detection of Staphylococcus aureus based on antibiotic-affinity strategy.

    PubMed

    Kong, Weijun; Xiong, Jie; Yue, Huan; Fu, Zhifeng

    2015-10-01

    A novel antibiotic-affinity strategy was designed for fluorimetric detection of pathogenic bacteria based on the strong affinity of antibiotic agent to the cell wall of bacteria. In this proof-of-concept work, vancocin, a glycopeptide antibiotic for Gram-positive bacteria, was used as a molecular recognition agent to anchor Staphylococcus aureus (S. aureus) cell. To improve the specificity of this method for S. aureus detection, IgG was adopted as the second recognition agent utilizing the binding between Fc region of IgG and S. aureus protein A in the cell wall, to form a sandwich complex. By using fluorescein isothiocyanate as the signal probe, S. aureus whole cells could be directly assayed within a linear range of 1.0 × 10(3)-1.0 × 10(9) CFU mL(-1) with a detection limit of 2.9 × 10(2) CFU mL(-1). The whole assay process could be completed within 130 min when a ready-for-use microplate was adopted. This proposed strategy for pathogenic bacteria detection possessed some attractive characteristics such as high sensitivity, wide linear range, simple manipulation, short assay time, and low cost. Furthermore, this sandwich mode also showed ideal specificity because vancocin and IgG bound with S. aureus at two distinct sites. It opened up a new pathway for high-throughput screening of pathogenic bacteria in medical diagnosis, food safety, bioterrorism defense, and drug discovery. PMID:26352835

  6. Binding affinity prediction of novel estrogen receptor ligands using receptor-based 3-D QSAR methods.

    PubMed

    Sippl, Wolfgang

    2002-12-01

    We have recently reported the development of a 3-D QSAR model for estrogen receptor ligands showing a significant correlation between calculated molecular interaction fields and experimentally measured binding affinity. The ligand alignment obtained from docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection procedure, a significant and robust model was obtained (q(2)(LOO)=0.921, SDEP=0.345). To further analyze the robustness and the predictivity of the established model several recently developed estrogen receptor ligands were selected as external test set. An excellent agreement between predicted and experimental binding data was obtained indicated by an external SDEP of 0.531. Two other traditionally used prediction techniques were applied in order to check the performance of the receptor-based 3-D QSAR procedure. The interaction energies calculated on the basis of receptor-ligand complexes were correlated with experimentally observed affinities. Also ligand-based 3-D QSAR models were generated using program FlexS. The interaction energy-based model, as well as the ligand-based 3-D QSAR models yielded models with lower predictivity. The comparison with the interaction energy-based model and with the ligand-based 3-D QSAR models, respectively, indicates that the combination of receptor-based and 3-D QSAR methods is able to improve the quality of prediction. PMID:12413831

  7. A Combined Method for Segmentation and Registration for an Advanced and Progressive Evaluation of Thermal Images

    PubMed Central

    Barcelos, Emilio Z.; Caminhas, Walmir M.; Ribeiro, Eraldo; Pimenta, Eduardo M.; Palhares, Reinaldo M.

    2014-01-01

    In this paper, a method that combines image analysis techniques, such as segmentation and registration, is proposed for an advanced and progressive evaluation of thermograms. The method is applied for the prevention of muscle injury in high-performance athletes, in collaboration with a Brazilian professional soccer club. The goal is to produce information on spatio-temporal variations of thermograms favoring the investigation of the athletes' conditions along the competition. The proposed method improves on current practice by providing a means for automatically detecting adaptive body-shaped regions of interest, instead of the manual selection of simple shapes. Specifically, our approach combines the optimization features in Otsu's method with a correction factor and post-processing techniques, enhancing thermal-image segmentation when compared to other methods. Additional contributions resulting from the combination of the segmentation and registration steps of our approach are the progressive analyses of thermograms in a unique spatial coordinate system and the accurate extraction of measurements and isotherms. PMID:25414972

  8. Uniscale multi-view registration using double dog-leg method

    NASA Astrophysics Data System (ADS)

    Chen, Chao-I.; Sargent, Dusty; Tsai, Chang-Ming; Wang, Yuan-Fang; Koppel, Dan

    2009-02-01

    3D computer models of body anatomy can have many uses in medical research and clinical practices. This paper describes a robust method that uses videos of body anatomy to construct multiple, partial 3D structures and then fuse them to form a larger, more complete computer model using the structure-from-motion framework. We employ the Double Dog-Leg (DDL) method, a trust-region based nonlinear optimization method, to jointly optimize the camera motion parameters (rotation and translation) and determine a global scale that all partial 3D structures should agree upon. These optimized motion parameters are used for constructing local structures, and the global scale is essential for multi-view registration after all these partial structures are built. In order to provide a good initial guess of the camera movement parameters and outlier free 2D point correspondences for DDL, we also propose a two-stage scheme where multi-RANSAC with a normalized eight-point algorithm is first performed and then a few iterations of an over-determined five-point algorithm is used to polish the results. Our experimental results using colonoscopy video show that the proposed scheme always produces more accurate outputs than the standard RANSAC scheme. Furthermore, since we have obtained many reliable point correspondences, time-consuming and error-prone registration methods like the iterative closest points (ICP) based algorithms can be replaced by a simple rigid-body transformation solver when merging partial structures into a larger model.

  9. Comparing multistep immobilized metal affinity chromatography and multistep TiO2 methods for phosphopeptide enrichment.

    PubMed

    Yue, Xiaoshan; Schunter, Alissa; Hummon, Amanda B

    2015-09-01

    Phosphopeptide enrichment from complicated peptide mixtures is an essential step for mass spectrometry-based phosphoproteomic studies to reduce sample complexity and ionization suppression effects. Typical methods for enriching phosphopeptides include immobilized metal affinity chromatography (IMAC) or titanium dioxide (TiO2) beads, which have selective affinity and can interact with phosphopeptides. In this study, the IMAC enrichment method was compared with the TiO2 enrichment method, using a multistep enrichment strategy from whole cell lysate, to evaluate their abilities to enrich for different types of phosphopeptides. The peptide-to-beads ratios were optimized for both IMAC and TiO2 beads. Both IMAC and TiO2 enrichments were performed for three rounds to enable the maximum extraction of phosphopeptides from the whole cell lysates. The phosphopeptides that are unique to IMAC enrichment, unique to TiO2 enrichment, and identified with both IMAC and TiO2 enrichment were analyzed for their characteristics. Both IMAC and TiO2 enriched similar amounts of phosphopeptides with comparable enrichment efficiency. However, phosphopeptides that are unique to IMAC enrichment showed a higher percentage of multiphosphopeptides as well as a higher percentage of longer, basic, and hydrophilic phosphopeptides. Also, the IMAC and TiO2 procedures clearly enriched phosphopeptides with different motifs. Finally, further enriching with two rounds of TiO2 from the supernatant after IMAC enrichment or further enriching with two rounds of IMAC from the supernatant TiO2 enrichment does not fully recover the phosphopeptides that are not identified with the corresponding multistep enrichment. PMID:26237447

  10. A comparative approach of four different image registration techniques for quantitative assessment of coronary artery calcium lesions using intravascular ultrasound.

    PubMed

    Araki, Tadashi; Ikeda, Nobutaka; Dey, Nilanjan; Chakraborty, Sayan; Saba, Luca; Kumar, Dinesh; Godia, Elisa Cuadrado; Jiang, Xiaoyi; Gupta, Ajay; Radeva, Petia; Laird, John R; Nicolaides, Andrew; Suri, Jasjit S

    2015-02-01

    In IVUS imaging, constant linear velocity and a constant angular velocity of 1800 rev/min causes displacement of the calcium in subsequent image frames. To overcome this error in intravascular ultrasound video, IVUS image frames must be registered prior to the lesion quantification. This paper presents a comprehensive comparison of four registration methods, namely: Rigid, Affine, B-Splines and Demons on five set of calcium lesion quantification parameters namely: (i) the mean lesion area, (ii) mean lesion arc, (iii) mean lesion span, (iv) mean lesion length, and (v) mean lesion distance from catheter. Using our IRB approved data of 100 patient volumes, our results shows that all four registrations showed a decrease in five calcium lesion parameters as follows: for Rigid registration, the values were: 4.92%, 5.84%, 5.89%, 5.27%, and 4.57%, respectively, for Affine registration the values were: 6.06%, 6.51%, 7.28%, 6.50%, and 5.94%, respectively, for B-Splines registration the values were: 7.35%, 8.03%, 9.54%, 8.18%, and 7.62%, respectively, and for Demons registration the five parameters were 7.32%, 8.02%, 10.11%, 7.94%, and 8.92% respectively. The relative overlap of identified lesions decreased by 5.91% in case of Rigid registration, 6.23% in case of Affine registration, 4.48% for Demons registration, whereas it increased by 3.05% in case of B-Splines registration. Rigid and Affine transformation-based registration took only 0.1936 and 0.2893 s per frame, respectively. Demons and B-Splines framework took only 0.5705 and 0.9405 s per frame, respectively, which were significantly slower than Rigid and Affine transformation based image registration. PMID:25523233

  11. Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes.

    PubMed

    Geng, Cunliang; Vangone, Anna; Bonvin, Alexandre M J J

    2016-08-01

    Reliable prediction of binding affinity changes (ΔΔG) upon mutations in protein complexes relies not only on the performance of computational methods but also on the availability and quality of experimental data. Binding affinity changes can be measured by various experimental methods with different accuracies and limitations. To understand the impact of these on the prediction of binding affinity change, we present the Database of binding Affinity Change Upon Mutation (DACUM), a database of 1872 binding affinity changes upon single-point mutations, a subset of the SKEMPI database (Moal,I.H. and Fernández-Recio,J. Bioinformatics, 2012;28:2600-2607) extended with information on the experimental methods used for ΔΔG measurements. The ΔΔG data were classified into different data sets based on the experimental method used and the position of the mutation (interface and non-interface). We tested the prediction performance of the original HADDOCK score, a newly trained version of it and mutation Cutoff Scanning Matrix (Pires,D.E.V., Ascher,D.B. and Blundell,T.L. Bioinformatics 2014;30:335-342), one of the best reported ΔΔG predictors so far, on these various data sets. Our results demonstrate a strong impact of the experimental methods on the performance of binding affinity change predictors for protein complexes. This underscores the importance of properly considering and carefully choosing experimental methods in the development of novel binding affinity change predictors. The DACUM database is available online at https://github.com/haddocking/DACUM. PMID:27284087

  12. Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method

    PubMed Central

    Bengtsson, Henrik; Hössjer, Ola

    2006-01-01

    Background Low-level processing and normalization of microarray data are most important steps in microarray analysis, which have profound impact on downstream analysis. Multiple methods have been suggested to date, but it is not clear which is the best. It is therefore important to further study the different normalization methods in detail and the nature of microarray data in general. Results A methodological study of affine models for gene expression data is carried out. Focus is on two-channel comparative studies, but the findings generalize also to single- and multi-channel data. The discussion applies to spotted as well as in-situ synthesized microarray data. Existing normalization methods such as curve-fit ("lowess") normalization, parallel and perpendicular translation normalization, and quantile normalization, but also dye-swap normalization are revisited in the light of the affine model and their strengths and weaknesses are investigated in this context. As a direct result from this study, we propose a robust non-parametric multi-dimensional affine normalization method, which can be applied to any number of microarrays with any number of channels either individually or all at once. A high-quality cDNA microarray data set with spike-in controls is used to demonstrate the power of the affine model and the proposed normalization method. Conclusion We find that an affine model can explain non-linear intensity-dependent systematic effects in observed log-ratios. Affine normalization removes such artifacts for non-differentially expressed genes and assures that symmetry between negative and positive log-ratios is obtained, which is fundamental when identifying differentially expressed genes. In addition, affine normalization makes the empirical distributions in different channels more equal, which is the purpose of quantile normalization, and may also explain why dye-swap normalization works or fails. All methods are made available in the aroma package, which is

  13. A practical salient region feature based 3D multi-modality registration method for medical images

    NASA Astrophysics Data System (ADS)

    Hahn, Dieter A.; Wolz, Gabriele; Sun, Yiyong; Hornegger, Joachim; Sauer, Frank; Kuwert, Torsten; Xu, Chenyang

    2006-03-01

    We present a novel representation of 3D salient region features and its integration into a hybrid rigid-body registration framework. We adopt scale, translation and rotation invariance properties of those intrinsic 3D features to estimate a transform between underlying mono- or multi-modal 3D medical images. Our method combines advantageous aspects of both feature- and intensity-based approaches and consists of three steps: an automatic extraction of a set of 3D salient region features on each image, a robust estimation of correspondences and their sub-pixel accurate refinement with outliers elimination. We propose a region-growing based approach for the extraction of 3D salient region features, a solution to the problem of feature clustering and a reduction of the correspondence search space complexity. Results of the developed algorithm are presented for both mono- and multi-modal intra-patient 3D image pairs (CT, PET and SPECT) that have been acquired for change detection, tumor localization, and time based intra-person studies. The accuracy of the method is clinically evaluated by a medical expert with an approach that measures the distance between a set of selected corresponding points consisting of both anatomical and functional structures or lesion sites. This demonstrates the robustness of the proposed method to image overlap, missing information and artefacts. We conclude by discussing potential medical applications and possibilities for integration into a non-rigid registration framework.

  14. An automatic high precision registration method between large area aerial images and aerial light detection and ranging data

    NASA Astrophysics Data System (ADS)

    Du, Q.; Xie, D.; Sun, Y.

    2015-06-01

    The integration of digital aerial photogrammetry and Light Detetion And Ranging (LiDAR) is an inevitable trend in Surveying and Mapping field. We calculate the external orientation elements of images which identical with LiDAR coordinate to realize automatic high precision registration between aerial images and LiDAR data. There are two ways to calculate orientation elements. One is single image spatial resection using image matching 3D points that registered to LiDAR. The other one is Position and Orientation System (POS) data supported aerotriangulation. The high precision registration points are selected as Ground Control Points (GCPs) instead of measuring GCPs manually during aerotriangulation. The registration experiments indicate that the method which registering aerial images and LiDAR points has a great advantage in higher automation and precision compare with manual registration.

  15. A bounded iterative closest point method for minimally invasive registration of the femur.

    PubMed

    Rodriguez y Baena, Ferdinando; Hawke, Trevor; Jakopec, Matjaz

    2013-10-01

    This article describes a novel method for image-based, minimally invasive registration of the femur, for application to computer-assisted unicompartmental knee arthroplasty. The method is adapted from the well-known iterative closest point algorithm. By utilising an estimate of the hip centre on both the preoperative model and intraoperative patient anatomy, the proposed 'bounded' iterative closest point algorithm robustly produces accurate varus-valgus and anterior-posterior femoral alignment with minimal distal access requirements. Similar to the original iterative closest point implementation, the bounded iterative closest point algorithm converges monotonically to the closest minimum, and the presented case includes a common method for global minimum identification. The bounded iterative closest point method has shown to have exceptional resistance to noise during feature acquisition through simulations and in vitro plastic bone trials, where its performance is compared to a standard form of the iterative closest point algorithm. PMID:23959859

  16. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods.

    PubMed

    Ryde, Ulf; Söderhjelm, Pär

    2016-05-11

    One of the largest challenges of computational chemistry is calculation of accurate free energies for the binding of a small molecule to a biological macromolecule, which has immense implications in drug development. It is well-known that standard molecular-mechanics force fields used in most such calculations have a limited accuracy. Therefore, there has been a great interest in improving the estimates using quantum-mechanical (QM) methods. We review here approaches involving explicit QM energies to calculate binding affinities, with an emphasis on the methods, rather than on specific applications. Many different QM methods have been employed, ranging from semiempirical QM calculations, via density-functional theory, to strict coupled-cluster calculations. Dispersion and other empirical corrections are mandatory for the approximate methods, as well as large basis sets for the stricter methods. QM has been used for the ligand, for a few crucial groups around the ligand, for all the closest atoms (200-1000 atoms), or for the full receptor-ligand complex, but it is likely that with a proper embedding it might be enough to include all groups within ∼6 Å of the ligand. Approaches involving minimized structures, simulations of the end states of the binding reaction, or full free-energy simulations have been tested. PMID:27077817

  17. Comparison of template registration methods for multi-site meta-analysis of brain morphometry

    NASA Astrophysics Data System (ADS)

    Faskowitz, Joshua; de Zubicaray, Greig I.; McMahon, Katie L.; Wright, Margaret J.; Thompson, Paul M.; Jahanshad, Neda

    2016-03-01

    Neuroimaging consortia such as ENIGMA can significantly improve power to discover factors that affect the human brain by pooling statistical inferences across cohorts to draw generalized conclusions from populations around the world. Voxelwise analyses such as tensor-based morphometry also allow an unbiased search for effects throughout the brain. Even so, such consortium-based analyses are limited by a lack of high-powered methods to harmonize voxelwise information across study populations and scanners. While the simplest approach may be to map all images to a single standard space, the benefits of cohort-specific templates have long been established. Here we studied methods to pool voxel-wise data across sites using templates customized for each cohort but providing a meaningful common space across all studies for voxelwise comparisons. As non-linear 3D MRI registrations represent mappings between images at millimeter resolution, we need to consider the reliability of these mappings. To evaluate these mappings, we calculated test-retest statistics on the volumetric maps of expansion and contraction. Further, we created study-specific brain templates for ten T1-weighted MRI datasets, and a common space from four study-specific templates. We evaluated the efficacy of using a two-step registration framework versus a single standard space. We found that the two-step framework more reliably mapped subjects to a common space.

  18. Note: A simple image processing based fiducial auto-alignment method for sample registration.

    PubMed

    Robertson, Wesley D; Porto, Lucas R; Ip, Candice J X; Nantel, Megan K T; Tellkamp, Friedjof; Lu, Yinfei; Miller, R J Dwayne

    2015-08-01

    A simple method for the location and auto-alignment of sample fiducials for sample registration using widely available MATLAB/LabVIEW software is demonstrated. The method is robust, easily implemented, and applicable to a wide variety of experiment types for improved reproducibility and increased setup speed. The software uses image processing to locate and measure the diameter and center point of circular fiducials for distance self-calibration and iterative alignment and can be used with most imaging systems. The method is demonstrated to be fast and reliable in locating and aligning sample fiducials, provided here by a nanofabricated array, with accuracy within the optical resolution of the imaging system. The software was further demonstrated to register, load, and sample the dynamically wetted array. PMID:26329245

  19. A Bayesian nonrigid registration method to enhance intraoperative target definition in image-guided prostate procedures through uncertainty characterization

    SciTech Connect

    Pursley, Jennifer; Risholm, Petter; Fedorov, Andriy; Tuncali, Kemal; Fennessy, Fiona M.; Wells, William M. III; Tempany, Clare M.; Cormack, Robert A.

    2012-11-15

    Purpose: This study introduces a probabilistic nonrigid registration method for use in image-guided prostate brachytherapy. Intraoperative imaging for prostate procedures, usually transrectal ultrasound (TRUS), is typically inferior to diagnostic-quality imaging of the pelvis such as endorectal magnetic resonance imaging (MRI). MR images contain superior detail of the prostate boundaries and provide substructure features not otherwise visible. Previous efforts to register diagnostic prostate images with the intraoperative coordinate system have been deterministic and did not offer a measure of the registration uncertainty. The authors developed a Bayesian registration method to estimate the posterior distribution on deformations and provide a case-specific measure of the associated registration uncertainty. Methods: The authors adapted a biomechanical-based probabilistic nonrigid method to register diagnostic to intraoperative images by aligning a physician's segmentations of the prostate in the two images. The posterior distribution was characterized with a Markov Chain Monte Carlo method; the maximum a posteriori deformation and the associated uncertainty were estimated from the collection of deformation samples drawn from the posterior distribution. The authors validated the registration method using a dataset created from ten patients with MRI-guided prostate biopsies who had both diagnostic and intraprocedural 3 Tesla MRI scans. The accuracy and precision of the estimated posterior distribution on deformations were evaluated from two predictive distance distributions: between the deformed central zone-peripheral zone (CZ-PZ) interface and the physician-labeled interface, and based on physician-defined landmarks. Geometric margins on the registration of the prostate's peripheral zone were determined from the posterior predictive distance to the CZ-PZ interface separately for the base, mid-gland, and apical regions of the prostate. Results: The authors observed

  20. An extended affinity propagation clustering method based on different data density types.

    PubMed

    Zhao, XiuLi; Xu, WeiXiang

    2015-01-01

    Affinity propagation (AP) algorithm, as a novel clustering method, does not require the users to specify the initial cluster centers in advance, which regards all data points as potential exemplars (cluster centers) equally and groups the clusters totally by the similar degree among the data points. But in many cases there exist some different intensive areas within the same data set, which means that the data set does not distribute homogeneously. In such situation the AP algorithm cannot group the data points into ideal clusters. In this paper, we proposed an extended AP clustering algorithm to deal with such a problem. There are two steps in our method: firstly the data set is partitioned into several data density types according to the nearest distances of each data point; and then the AP clustering method is, respectively, used to group the data points into clusters in each data density type. Two experiments are carried out to evaluate the performance of our algorithm: one utilizes an artificial data set and the other uses a real seismic data set. The experiment results show that groups are obtained more accurately by our algorithm than OPTICS and AP clustering algorithm itself. PMID:25685144

  1. Quantitative evaluation of an image registration method for a NIPAM gel dosimeter

    NASA Astrophysics Data System (ADS)

    Chang, Yuan-Jen; Yao, Chun-Hsu; Wu, Jay; Hsieh, Bor-Tsung; Tsang, Yuk-Wah; Chen, Chin-Hsing

    2015-06-01

    One of the problems in obtaining quality results is image registration when a gel dosimeter is used in conjunction with optical computed tomography (CT). This study proposes a passive alignment mechanism to obtain a precisely measured dose map. A holder plate with two pin-hole pairs is placed on the gel container cap. These two pin-hole pairs attach the gel container to the vertical shaft and can be precisely aligned with the rotation center of the vertical shaft at any time. Accordingly, a better reconstructed image quality is obtained. After obtaining a precisely measured dose map, the scale invariant feature transform (SIFT)-flow algorithm is utilized as an image registration method to align the treatment plan software (TPS) image with the measured dose map image. The results show that the gamma pass rate for the single-field irradiation increases from 83.39% to 94.03% when the algorithm is applied. And the gamma pass rate for the five-field irradiation treatment plan increases from 87.36% to 94.34%. The translation, scaling, and rotation occurring in the dose map image constructed using an optical CT scanner are also aligned with those in the TPS image using the SIFT-flow algorithm. Accordingly, improved gamma comparison results and a higher gamma pass rate are obtained.

  2. Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules III: A Benchmark of GW Methods.

    PubMed

    Knight, Joseph W; Wang, Xiaopeng; Gallandi, Lukas; Dolgounitcheva, Olga; Ren, Xinguo; Ortiz, J Vincent; Rinke, Patrick; Körzdörfer, Thomas; Marom, Noa

    2016-02-01

    The performance of different GW methods is assessed for a set of 24 organic acceptors. Errors are evaluated with respect to coupled cluster singles, doubles, and perturbative triples [CCSD(T)] reference data for the vertical ionization potentials (IPs) and electron affinities (EAs), extrapolated to the complete basis set limit. Additional comparisons are made to experimental data, where available. We consider fully self-consistent GW (scGW), partial self-consistency in the Green's function (scGW0), non-self-consistent G0W0 based on several mean-field starting points, and a "beyond GW" second-order screened exchange (SOSEX) correction to G0W0. We also describe the implementation of the self-consistent Coulomb hole with screened exchange method (COHSEX), which serves as one of the mean-field starting points. The best performers overall are G0W0+SOSEX and G0W0 based on an IP-tuned long-range corrected hybrid functional with the former being more accurate for EAs and the latter for IPs. Both provide a balanced treatment of localized vs delocalized states and valence spectra in good agreement with photoemission spectroscopy (PES) experiments. PMID:26731609

  3. Ligand affinity chromatography, an indispensable method for the purification of soluble cytokine receptors and binding proteins.

    PubMed

    Novick, Daniela; Rubinstein, Menachem

    2012-01-01

    Ligand affinity chromatography separation is based on unique interaction between the target analyte and a ligand, which is coupled covalently to a resin. It is a simple, rapid, selective, and efficient purification procedure of proteins providing tens of thousands fold purification in one step. The biological activity of the isolated proteins is retained in most cases thus function is revealed concomitantly with the isolation. Prior to the completion of the genome project this method facilitated rapid and reliable cloning of the corresponding gene. Upon completion of this project, a partial protein sequence is enough for retrieving its complete mRNA and hence its complete protein sequence. This method is indispensable for the isolation of both expected (e.g. receptors) but mainly unexpected, unpredicted and very much surprising binding proteins. No other approach would yield the latter. This chapter provides examples for both the expected target proteins, isolated from rich sources of human proteins, as well as the unexpected binding proteins, found by serendipity. PMID:22131033

  4. A general method of community detection by identifying community centers with affinity propagation

    NASA Astrophysics Data System (ADS)

    Guo, Wei-Feng; Zhang, Shao-Wu

    2016-04-01

    Detection of community structures is beneficial to analyzing the structures and properties of networks. It is of theoretical interest and practical significance in modern science. So far, a large number of algorithms have been proposed to detect community structures in complex networks, but most of them are suitable for a specific network structure. In this paper, a novel method (called CDMIC) is proposed to detect the communities in un-weighted, weighted, un-directed, directed and signed networks by constructing a dissimilarity distance matrix of network and identifying community centers with maximizing modularity. For a given network, we first estimate the distance between all pairs of nodes for constructing the dissimilarity distance matrix of the network. Then, this distance matrix is input to the affinity propagation (AP) algorithm to extract a candidate center set of community. Thirdly, we rank these centers in descending order according to the sum of their availability and responsibility. Finally, we determine the community structure by selecting the center subset from the candidate center set in an incremental manner to make the modularity maximization. On three real-world networks and some synthetic networks, experimental results show that our CDMIC method has higher performance in terms of classification accuracy and normalized mutual information (NMI), and ability to tolerate the resolution limitation.

  5. Method for performing site-specific affinity fractionation for use in DNA sequencing

    DOEpatents

    Mirzabekov, A.D.; Lysov, Y.P.; Dubley, S.A.

    1999-05-18

    A method for fractionating and sequencing DNA via affinity interaction is provided comprising contacting cleaved DNA to a first array of oligonucleotide molecules to facilitate hybridization between the cleaved DNA and the molecules; extracting the hybridized DNA from the molecules; contacting the extracted hybridized DNA with a second array of oligonucleotide molecules, wherein the oligonucleotide molecules in the second array have specified base sequences that are complementary to the extracted hybridized DNA; and attaching labeled DNA to the second array of oligonucleotide molecules, wherein the labeled re-hybridized DNA have sequences that are complementary to the oligomers. The invention further provides a method for performing multi-step conversions of the chemical structure of compounds comprising supplying an array of polyacrylamide vessels separated by hydrophobic surfaces; immobilizing a plurality of reactants, such as enzymes, in the vessels so that each vessel contains one reactant; contacting the compounds to each of the vessels in a predetermined sequence and for a sufficient time to convert the compounds to a desired state; and isolating the converted compounds from the array. 14 figs.

  6. Method for performing site-specific affinity fractionation for use in DNA sequencing

    DOEpatents

    Mirzabekov, Andrei Darievich; Lysov, Yuri Petrovich; Dubley, Svetlana A.

    1999-01-01

    A method for fractionating and sequencing DNA via affinity interaction is provided comprising contacting cleaved DNA to a first array of oligonucleotide molecules to facilitate hybridization between said cleaved DNA and the molecules; extracting the hybridized DNA from the molecules; contacting said extracted hybridized DNA with a second array of oligonucleotide molecules, wherein the oligonucleotide molecules in the second array have specified base sequences that are complementary to said extracted hybridized DNA; and attaching labeled DNA to the second array of oligonucleotide molecules, wherein the labeled re-hybridized DNA have sequences that are complementary to the oligomers. The invention further provides a method for performing multi-step conversions of the chemical structure of compounds comprising supplying an array of polyacrylamide vessels separated by hydrophobic surfaces; immobilizing a plurality of reactants, such as enzymes, in the vessels so that each vessel contains one reactant; contacting the compounds to each of the vessels in a predetermined sequence and for a sufficient time to convert the compounds to a desired state; and isolating the converted compounds from said array.

  7. 32 CFR 1615.1 - Registration.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Registration. 1615.1 Section 1615.1 National... REGISTRATION § 1615.1 Registration. (a) Registration under selective service law consists of: (1) Completing a registration card or other method of registration prescribed by the Director of Selective Service by a...

  8. 32 CFR 1615.1 - Registration.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 6 2011-07-01 2011-07-01 false Registration. 1615.1 Section 1615.1 National... REGISTRATION § 1615.1 Registration. (a) Registration under selective service law consists of: (1) Completing a registration card or other method of registration prescribed by the Director of Selective Service by a...

  9. Surface Plasmon Resonance Biosensor Method for Palytoxin Detection Based on Na+,K+-ATPase Affinity

    PubMed Central

    Alfonso, Amparo; Pazos, María-José; Fernández-Araujo, Andrea; Tobio, Araceli; Alfonso, Carmen; Vieytes, Mercedes R.; Botana, Luis M.

    2013-01-01

    Palytoxin (PLTX), produced by dinoflagellates from the genus Ostreopsis was first discovered, isolated, and purified from zoanthids belonging to the genus Palythoa. The detection of this toxin in contaminated shellfish is essential for human health preservation. A broad range of studies indicate that mammalian Na+,K+-ATPase is a high affinity cellular receptor for PLTX. The toxin converts the pump into an open channel that stimulates sodium influx and potassium efflux. In this work we develop a detection method for PLTX based on its binding to the Na+,K+-ATPase. The method was developed by using the phenomenon of surface plasmon resonance (SPR) to monitor biomolecular reactions. This technique does not require any labeling of components. The interaction of PLTX over immobilized Na+,K+-ATPase is quantified by injecting different concentrations of toxin in the biosensor and checking the binding rate constant (kobs). From the representation of kobs versus PLTX concentration, the kinetic equilibrium dissociation constant (KD) for the PLTX-Na+,K+-ATPase association can be calculated. The value of this constant is KD = 6.38 × 10−7 ± 6.67 × 10−8 M PLTX. In this way the PLTX-Na+,K+-ATPase association was used as a suitable method for determination of the toxin concentration in a sample. This method represents a new and useful approach to easily detect the presence of PLTX-like compounds in marine products using the mechanism of action of these toxins and in this way reduce the use of other more expensive and animal based methods. PMID:24379088

  10. Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

    SciTech Connect

    Zhao, Huaying Schuck, Peter

    2015-01-01

    Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of the stoichiometry, affinity and cooperativity of multi-site interactions. The principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT are reviewed, their complementarity in GMMA is described and a new GMMA simulation tool set in SEDPHAT is presented. Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design.

  11. PSO-based methods for medical image registration and change assessment of pigmented skin

    NASA Astrophysics Data System (ADS)

    Kacenjar, Steve; Zook, Matthew; Balint, Michael

    2011-03-01

    There are various scientific and technological areas in which it is imperative to rapidly detect and quantify changes in imagery over time. In fields such as earth remote sensing, aerospace systems, and medical imaging, searching for timedependent, regional changes across deformable topographies is complicated by varying camera acquisition geometries, lighting environments, background clutter conditions, and occlusion. Under these constantly-fluctuating conditions, the use of standard, rigid-body registration approaches often fail to provide sufficient fidelity to overlay image scenes together. This is problematic because incorrect assessments of the underlying changes of high-level topography can result in systematic errors in the quantification and classification of interested areas. For example, in the current naked-eye detection strategies of melanoma, a dermatologist often uses static morphological attributes to identify suspicious skin lesions for biopsy. This approach does not incorporate temporal changes which suggest malignant degeneration. By performing the co-registration of time-separated skin imagery, a dermatologist may more effectively detect and identify early morphological changes in pigmented lesions; enabling the physician to detect cancers at an earlier stage resulting in decreased morbidity and mortality. This paper describes an image processing system which will be used to detect changes in the characteristics of skin lesions over time. The proposed system consists of three main functional elements: 1.) coarse alignment of timesequenced imagery, 2.) refined alignment of local skin topographies, and 3.) assessment of local changes in lesion size. During the coarse alignment process, various approaches can be used to obtain a rough alignment, including: 1.) a manual landmark/intensity-based registration method1, and 2.) several flavors of autonomous optical matched filter methods2. These procedures result in the rough alignment of a patient

  12. A computationally efficient method for automatic registration of orthogonal x-ray images with volumetric CT data

    NASA Astrophysics Data System (ADS)

    Chen, Xin; Varley, Martin R.; Shark, Lik-Kwan; Shentall, Glyn S.; Kirby, Mike C.

    2008-02-01

    The paper presents a computationally efficient 3D-2D image registration algorithm for automatic pre-treatment validation in radiotherapy. The novel aspects of the algorithm include (a) a hybrid cost function based on partial digitally reconstructed radiographs (DRRs) generated along projected anatomical contours and a level set term for similarity measurement; and (b) a fast search method based on parabola fitting and sensitivity-based search order. Using CT and orthogonal x-ray images from a skull and a pelvis phantom, the proposed algorithm is compared with the conventional ray-casting full DRR based registration method. Not only is the algorithm shown to be computationally more efficient with registration time being reduced by a factor of 8, but also the algorithm is shown to offer 50% higher capture range allowing the initial patient displacement up to 15 mm (measured by mean target registration error). For the simulated data, high registration accuracy with average errors of 0.53 mm ± 0.12 mm for translation and 0.61° ± 0.29° for rotation within the capture range has been achieved. For the tested phantom data, the algorithm has also shown to be robust without being affected by artificial markers in the image.

  13. Robust image registration of biological microscopic images.

    PubMed

    Wang, Ching-Wei; Ka, Shuk-Man; Chen, Ann

    2014-01-01

    Image registration of biological data is challenging as complex deformation problems are common. Possible deformation effects can be caused in individual data preparation processes, involving morphological deformations, stain variations, stain artifacts, rotation, translation, and missing tissues. The combining deformation effects tend to make existing automatic registration methods perform poor. In our experiments on serial histopathological images, the six state of the art image registration techniques, including TrakEM2, SURF + affine transformation, UnwarpJ, bUnwarpJ, CLAHE + bUnwarpJ and BrainAligner, achieve no greater than 70% averaged accuracies, while the proposed method achieves 91.49% averaged accuracy. The proposed method has also been demonstrated to be significantly better in alignment of laser scanning microscope brain images and serial ssTEM images than the benchmark automatic approaches (p < 0.001). The contribution of this study is to introduce a fully automatic, robust and fast image registration method for 2D image registration. PMID:25116443

  14. Nonrigid registration method to assess reproducibility of breath-holding with ABC in lung cancer

    SciTech Connect

    Sarrut, David . E-mail: dsarrut@univ-lyon2.fr; Boldea, Vlad; Ayadi, Myriam; Badel, Jean-Noel; Ginestet, Chantal; Clippe, Sebastien; Carrie, Christian

    2005-02-01

    Purpose: To study the interfraction reproducibility of breath-holding using active breath control (ABC), and to develop computerized tools to evaluate three-dimensional (3D) intrathoracic motion in each patient. Methods and materials: Since June 2002, 11 patients with non-small-cell lung cancer enrolled in a Phase II trial have undergone four CT scans: one during free-breathing (reference) and three using ABC. Patients left the room between breath-hold scans. The patient's breath was held at the same predefined phase of the breathing cycle (about 70% of the vital capacity) using the ABC device, then patients received 3D-conformal radiotherapy. Automated computerized tools for breath-hold CT scans were developed to analyze lung and tumor interfraction residual motions with 3D nonrigid registration. Results: All patients but one were safely treated with ABC for 7 weeks. For 6 patients, the lung volume differences were <5%. The mean 3D displacement inside the lungs was between 2.3 mm (SD 1.4) and 4 mm (SD 3.3), and the gross tumor volume residual motion was 0.9 mm (SD 0.4) to 5.9 mm (SD 0.7). The residual motion was slightly greater in the inferior part of the lung than the superior. For 2 patients, we detected volume changes >300 cm{sup 3} and displacements >10 mm, probably owing to atelectasia and emphysema. One patient was excluded, and two others had incomplete data sets. Conclusion: Breath-holding with ABC was effective in 6 patients, and discrepancies were clinically accountable in 2. The proposed 3D nonrigid registration method allows for personalized evaluation of breath-holding reproducibility with ABC. It will be used to adapt the patient-specific internal margins.

  15. Scene-based nonuniformity correction using multiframe registration and iteration method

    NASA Astrophysics Data System (ADS)

    Ren, Jianle; Chen, Qian; Qian, Weixian; Yu, Xuelian; Li, Danping

    2014-05-01

    In this paper, an improved scene-based nonuniformity correction (NC) algorithm for infrared focal plane arrays (IRFPAs) using multiframe registration and iteration method is proposed. This method estimates the global translation and iterates between several adjacent frames. Then mean square error between any two properly registered images is minimized to obtain nonuniformity correction parameters. The detailed method includes three main steps: First, we assume that brightness along the motion trajectory is constant, and a linear detector response and model the nonuniformity of each detector with a gain and a bias. Second, several adjacent frames are used to compute relative motion of any two adjacent frames. Here we use the Fourier shift theorem, their relative translation can be obtained by calculating their normalized cross-power spectrum. We choose K adjacent frames, so the total number of iteration is K*(K-1)/2. Then the mean square error function is defined as the corresponding difference between the two adjacent corrected frames, and it is minimized making use of the least mean square algorithm. The use of correlation of adjacent frames sufficiently, together with iteration strategy between them, can get fast and reliable fixed-pattern noise reduction with low few ghosting artifacts. We define the algorithm and present a number of experimental results to demonstrate the efficacy of the proposed method in comparison to several previously published methods. The performance of the proposed method is thoroughly evaluated with clean infrared image sequences with synthetic nonuniformity and real infrared imagery.

  16. Automatic Registration between Real-Time Ultrasonography and Pre-Procedural Magnetic Resonance Images: A Prospective Comparison between Two Registration Methods by Liver Surface and Vessel and by Liver Surface Only.

    PubMed

    Kim, Ah Yeong; Lee, Min Woo; Cha, Dong Ik; Lim, Hyo Keun; Oh, Young-Taek; Jeong, Ja-Yeon; Chang, Jung-Woo; Ryu, Jiwon; Lee, Kyong Joon; Kim, Jaeil; Bang, Won-Chul; Shin, Dong Kuk; Choi, Sung Jin; Koh, Dalkwon; Seo, Bong Koo; Kim, Kyunga

    2016-07-01

    The aim of this study was to compare the accuracy of and the time required for image fusion between real-time ultrasonography (US) and pre-procedural magnetic resonance (MR) images using automatic registration by a liver surface only method and automatic registration by a liver surface and vessel method. This study consisted of 20 patients referred for planning US to assess the feasibility of percutaneous radiofrequency ablation or biopsy for focal hepatic lesions. The first 10 consecutive patients were evaluated by an experienced radiologist using the automatic registration by liver surface and vessel method, whereas the remaining 10 patients were evaluated using the automatic registration by liver surface only method. For all 20 patients, image fusion was automatically executed after following the protocols and fused real-time US and MR images moved synchronously. The accuracy of each method was evaluated by measuring the registration error, and the time required for image fusion was assessed by evaluating the recorded data using in-house software. The results obtained using the two automatic registration methods were compared using the Mann-Whitney U-test. Image fusion was successful in all 20 patients, and the time required for image fusion was significantly shorter with the automatic registration by liver surface only method than with the automatic registration by liver surface and vessel method (median: 43.0 s, range: 29-74 s vs. median: 83.0 s, range: 46-101 s; p = 0.002). The registration error did not significantly differ between the two methods (median: 4.0 mm, range: 2.1-9.9 mm vs. median: 3.7 mm, range: 1.8-5.2 mm; p = 0.496). The automatic registration by liver surface only method offers faster image fusion between real-time US and pre-procedural MR images than does the automatic registration by liver surface and vessel method. However, the degree of accuracy was similar for the two methods. PMID:27085384

  17. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site

    PubMed Central

    Boyce, Sarah E.; Mobley, David L.; Rocklin, Gabriel; Graves, Alan P.

    2009-01-01

    We present a combined experimental and modeling study of organic ligand molecules binding to a slightly polar engineered cavity site in T4 lysozyme (L99A/M102Q). For modeling, we computed alchemical absolute binding free energies. These were blind tests performed prospectively on 13 diverse, previously untested candidate ligand molecules. We predicted that eight compounds would bind to the cavity and five would not; 11 of 13 predictions were correct at this level. The RMS error to the measurable absolute binding energies was 1.8 kcal/mol. In addition, we computed relative binding free energies for six phenol derivatives starting from two known ligands: phenol and catechol. The average RMS error in the relative free energy prediction was 2.5 (phenol) and 1.1 (catechol) kcal/mol. To understand these results at atomic resolution, we obtained x-ray co-complex structures for nine of the diverse ligands and for all six phenol analogs. The average RMSD of the predicted pose to the experiment was 2.0Å (diverse set), 1.8Å (phenol derived predictions) and 1.2Å (catechol derived predictions). We found that to predict accurate affinities and rank-orderings required near-native starting orientations of the ligand in the binding site. Unanticipated binding modes, multiple ligand binding, and protein conformational change all proved challenging for the free energy methods. We believe these results can help guide future improvements in physics-based absolute binding free energy methods. PMID:19782087

  18. Medical image registration using machine learning-based interest point detector

    NASA Astrophysics Data System (ADS)

    Sergeev, Sergey; Zhao, Yang; Linguraru, Marius George; Okada, Kazunori

    2012-02-01

    This paper presents a feature-based image registration framework which exploits a novel machine learning (ML)-based interest point detection (IPD) algorithm for feature selection and correspondence detection. We use a feed-forward neural network (NN) with back-propagation as our base ML detector. Literature on ML-based IPD is scarce and to our best knowledge no previous research has addressed feature selection strategy for IPD purpose with cross-validation (CV) detectability measure. Our target application is the registration of clinical abdominal CT scans with abnormal anatomies. We evaluated the correspondence detection performance of the proposed ML-based detector against two well-known IPD algorithms: SIFT and SURF. The proposed method is capable of performing affine rigid registrations of 2D and 3D CT images, demonstrating more than two times better accuracy in correspondence detection than SIFT and SURF. The registration accuracy has been validated manually using identified landmark points. Our experimental results shows an improvement in 3D image registration quality of 18.92% compared with affine transformation image registration method from standard ITK affine registration toolkit.

  19. Registration and three-dimensional reconstruction of autoradiographic images by the disparity analysis method

    SciTech Connect

    Zhao, Weizhao; Ginsberg, M. . Cerebral Vascular Disease Research Center); Young, T.Y. . Dept. of Electrical and Computer Engineering)

    1993-12-01

    Quantitative autoradiography is a powerful radio-isotopic-imaging method for neuroscientists to study local cerebral blood flow and glucose-metabolic rate at rest, in response to physiologic activation of the visual, auditory, somatosensory, and motor systems, and in pathologic conditions. Most autoradiographic studies analyze glucose utilization and blood flow in two-dimensional (2-D) coronal sections. With modern digital computer and image-processing techniques, a large number of closely spaced coronal sections can be stacked appropriately to form a three-dimensional (3-d) image. 3-D autoradiography allows investigators to observe cerebral sections and surfaces from any viewing angle. A fundamental problem in 3-D reconstruction is the alignment (registration) of the coronal sections. A new alignment method based on disparity analysis is presented which can overcome many of the difficulties encountered by previous methods. The disparity analysis method can deal with asymmetric, damaged, or tilted coronal sections under the same general framework, and it can be used to match coronal sections of different sizes and shapes. Experimental results on alignment and 3-D reconstruction are presented.

  20. Practical pseudo-3D registration for large tomographic images

    NASA Astrophysics Data System (ADS)

    Liu, Xuan; Laperre, Kjell; Sasov, Alexander

    2014-09-01

    Image registration is a powerful tool in various tomographic applications. Our main focus is on microCT applications in which samples/animals can be scanned multiple times under different conditions or at different time points. For this purpose, a registration tool capable of handling fairly large volumes has been developed, using a novel pseudo-3D method to achieve fast and interactive registration with simultaneous 3D visualization. To reduce computation complexity in 3D registration, we decompose it into several 2D registrations, which are applied to the orthogonal views (transaxial, sagittal and coronal) sequentially and iteratively. After registration in each view, the next view is retrieved with the new transformation matrix for registration. This reduces the computation complexity significantly. For rigid transform, we only need to search for 3 parameters (2 shifts, 1 rotation) in each of the 3 orthogonal views instead of 6 (3 shifts, 3 rotations) for full 3D volume. In addition, the amount of voxels involved is also significantly reduced. For the proposed pseudo-3D method, image-based registration is employed, with Sum of Square Difference (SSD) as the similarity measure. The searching engine is Powell's conjugate direction method. In this paper, only rigid transform is used. However, it can be extended to affine transform by adding scaling and possibly shearing to the transform model. We have noticed that more information can be used in the 2D registration if Maximum Intensity Projections (MIP) or Parallel Projections (PP) is used instead of the orthogonal views. Also, other similarity measures, such as covariance or mutual information, can be easily incorporated. The initial evaluation on microCT data shows very promising results. Two application examples are shown: dental samples before and after treatment and structural changes in materials before and after compression. Evaluation on registration accuracy between pseudo-3D method and true 3D method has

  1. Diagnostic possibilities with multidimensional images in head and neck area using efficient registration and visualization methods

    NASA Astrophysics Data System (ADS)

    Zeilhofer, Hans-Florian U.; Krol, Zdzislaw; Sader, Robert; Hoffmann, Karl-Heinz; Gerhardt, Paul; Schweiger, Markus; Horch, Hans-Henning

    1997-05-01

    For several diseases in the head and neck area different imaging modalities are applied to the same patient.Each of these image data sets has its specific advantages and disadvantages. The combination of different methods allows to make the best use of the advantageous properties of each method while minimizing the impact of its negative aspects. Soft tissue alterations can be judged better in an MRI image while it may be unrecognizable in the relating CT. Bone tissue, on the other hand, is optimally imaged in CT. Inflammatory nuclei of the bone can be detected best by their increased signal in SPECT. Only the combination of all modalities let the physical come to an exact statement on pathological processes that involve multiple tissue structures. Several surfaces and voxel based matching functions we have tested allowed a precise merging by means of numerical optimization methods like e.g. simulated annealing without the complicated assertion of fiducial markers or the localization landmarks in 2D cross sectional slice images. The quality of the registration depends on the choice of the optimization procedure according to the complexity of the matching function landscape. Precise correlation of the multimodal head and neck area images together with its 2D and 3D presentation techniques provides a valuable tool for physicians.

  2. 2D and 3D registration methods for dual-energy contrast-enhanced digital breast tomosynthesis

    NASA Astrophysics Data System (ADS)

    Lau, Kristen C.; Roth, Susan; Maidment, Andrew D. A.

    2014-03-01

    Contrast-enhanced digital breast tomosynthesis (CE-DBT) uses an iodinated contrast agent to image the threedimensional breast vasculature. The University of Pennsylvania is conducting a CE-DBT clinical study in patients with known breast cancers. The breast is compressed continuously and imaged at four time points (1 pre-contrast; 3 postcontrast). A hybrid subtraction scheme is proposed. First, dual-energy (DE) images are obtained by a weighted logarithmic subtraction of the high-energy and low-energy image pairs. Then, post-contrast DE images are subtracted from the pre-contrast DE image. This hybrid temporal subtraction of DE images is performed to analyze iodine uptake, but suffers from motion artifacts. Employing image registration further helps to correct for motion, enhancing the evaluation of vascular kinetics. Registration using ANTS (Advanced Normalization Tools) is performed in an iterative manner. Mutual information optimization first corrects large-scale motions. Normalized cross-correlation optimization then iteratively corrects fine-scale misalignment. Two methods have been evaluated: a 2D method using a slice-by-slice approach, and a 3D method using a volumetric approach to account for out-of-plane breast motion. Our results demonstrate that iterative registration qualitatively improves with each iteration (five iterations total). Motion artifacts near the edge of the breast are corrected effectively and structures within the breast (e.g. blood vessels, surgical clip) are better visualized. Statistical and clinical evaluations of registration accuracy in the CE-DBT images are ongoing.

  3. Deep Adaptive Log-Demons: Diffeomorphic Image Registration with Very Large Deformations

    PubMed Central

    Zhao, Liya; Jia, Kebin

    2015-01-01

    This paper proposes a new framework for capturing large and complex deformation in image registration. Traditionally, this challenging problem relies firstly on a preregistration, usually an affine matrix containing rotation, scale, and translation and afterwards on a nonrigid transformation. According to preregistration, the directly calculated affine matrix, which is obtained by limited pixel information, may misregistrate when large biases exist, thus misleading following registration subversively. To address this problem, for two-dimensional (2D) images, the two-layer deep adaptive registration framework proposed in this paper firstly accurately classifies the rotation parameter through multilayer convolutional neural networks (CNNs) and then identifies scale and translation parameters separately. For three-dimensional (3D) images, affine matrix is located through feature correspondences by a triplanar 2D CNNs. Then deformation removal is done iteratively through preregistration and demons registration. By comparison with the state-of-the-art registration framework, our method gains more accurate registration results on both synthetic and real datasets. Besides, principal component analysis (PCA) is combined with correlation like Pearson and Spearman to form new similarity standards in 2D and 3D registration. Experiment results also show faster convergence speed. PMID:26120356

  4. Deep Adaptive Log-Demons: Diffeomorphic Image Registration with Very Large Deformations.

    PubMed

    Zhao, Liya; Jia, Kebin

    2015-01-01

    This paper proposes a new framework for capturing large and complex deformation in image registration. Traditionally, this challenging problem relies firstly on a preregistration, usually an affine matrix containing rotation, scale, and translation and afterwards on a nonrigid transformation. According to preregistration, the directly calculated affine matrix, which is obtained by limited pixel information, may misregistrate when large biases exist, thus misleading following registration subversively. To address this problem, for two-dimensional (2D) images, the two-layer deep adaptive registration framework proposed in this paper firstly accurately classifies the rotation parameter through multilayer convolutional neural networks (CNNs) and then identifies scale and translation parameters separately. For three-dimensional (3D) images, affine matrix is located through feature correspondences by a triplanar 2D CNNs. Then deformation removal is done iteratively through preregistration and demons registration. By comparison with the state-of-the-art registration framework, our method gains more accurate registration results on both synthetic and real datasets. Besides, principal component analysis (PCA) is combined with correlation like Pearson and Spearman to form new similarity standards in 2D and 3D registration. Experiment results also show faster convergence speed. PMID:26120356

  5. An efficient strategy based on an individualized selection of registration methods. Application to the coregistration of MR and SPECT images in neuro-oncology

    NASA Astrophysics Data System (ADS)

    Tacchella, Jean-Marc; Roullot, Elodie; Lefort, Muriel; Cohen, Mike-Ely; Guillevin, Rémy; Petrirena, Grégorio; Delattre, Jean-Yves; Habert, Marie-Odile; Yeni, Nathanaëlle; Kas, Aurélie; Frouin, Frédérique

    2014-11-01

    An efficient registration strategy is described that aims to help solve delicate medical imaging registration problems. It consists of running several registration methods for each dataset and selecting the best one for each specific dataset, according to an evaluation criterion. Finally, the quality of the registration results, obtained with the best method, is visually scored by an expert as excellent, correct or poor. The strategy was applied to coregister Technetium-99m Sestamibi SPECT and MRI data in the framework of a follow-up protocol in patients with high grade gliomas receiving antiangiogenic therapy. To adapt the strategy to this clinical context, a robust semi-automatic evaluation criterion based on the physiological uptake of the Sestamibi tracer was defined. A panel of eighteen multimodal registration algorithms issued from BrainVisa, SPM or AIR software environments was systematically applied to the clinical database composed of sixty-two datasets. According to the expert visual validation, this new strategy provides 85% excellent registrations, 12% correct ones and only 3% poor ones. These results compare favorably to the ones obtained by the globally most efficient registration method over the whole database, for which only 61% of excellent registration results have been reported. Thus the registration strategy in its current implementation proves to be suitable for clinical application.

  6. Multimodal registration of retinal images using self organizing maps.

    PubMed

    Matsopoulos, George K; Asvestas, Pantelis A; Mouravliansky, Nikolaos A; Delibasis, Konstantinos K

    2004-12-01

    In this paper, an automatic method for registering multimodal retinal images is presented. The method consists of three steps: the vessel centerline detection and extraction of bifurcation points only in the reference image, the automatic correspondence of bifurcation points in the two images using a novel implementation of the self organizing maps and the extraction of the parameters of the affine transform using the previously obtained correspondences. The proposed registration algorithm was tested on 24 multimodal retinal pairs and the obtained results show an advantageous performance in terms of accuracy with respect to the manual registration. PMID:15575412

  7. A sensitive and selective resonance Rayleigh scattering method for quick detection of avidin using affinity labeling Au nanoparticles

    NASA Astrophysics Data System (ADS)

    Wang, Qi; Huang, Xi; Fu, Xuan; Deng, Huan; Ma, Meihu; Cai, Zhaoxia

    2016-06-01

    Avidin is a glycoprotein with antinutritional property, which should be limited in daily food. We developed an affinity biosensor system based on resonance Rayleigh scattering (RRS) and using affinity biotin labeling Au nanoparticles (AuNPs). This method was selective and sensitive for quick avidin detection due to the avidin-biotin affinitive interaction. Under optimal conditions, RRS intensity of biotin-AuNPs increase linearly with an increasing concentration of avidin from 5 to 160 ng/mL. The lower limit of detection was 0.59 ng/mL. This rapid and selective avidin detection method was used in synthetic samples and egg products with recoveries of between 102.97 and 107.92%, thereby demonstrating the feasible and practical application of this assay.

  8. A sensitive and selective resonance Rayleigh scattering method for quick detection of avidin using affinity labeling Au nanoparticles.

    PubMed

    Wang, Qi; Huang, Xi; Fu, Xuan; Deng, Huan; Ma, Meihu; Cai, Zhaoxia

    2016-06-01

    Avidin is a glycoprotein with antinutritional property, which should be limited in daily food. We developed an affinity biosensor system based on resonance Rayleigh scattering (RRS) and using affinity biotin labeling Au nanoparticles (AuNPs). This method was selective and sensitive for quick avidin detection due to the avidin-biotin affinitive interaction. Under optimal conditions, RRS intensity of biotin-AuNPs increase linearly with an increasing concentration of avidin from 5 to 160ng/mL. The lower limit of detection was 0.59ng/mL. This rapid and selective avidin detection method was used in synthetic samples and egg products with recoveries of between 102.97 and 107.92%, thereby demonstrating the feasible and practical application of this assay. PMID:26978788

  9. Development and Validation of an Affinity Chromatography-Protein G Method for IgG Quantification

    PubMed Central

    Paradina Fernández, Lesly; Calvo, Loany; Viña, Lisel

    2014-01-01

    Nimotuzumab, an IgG that recognizes the epidermal growth factor receptor (EGF-R) overexpressed in some tumors, is used in the treatment of advanced head and neck cancer. For the quantification of this protein in cell culture supernatants, protein G-HPLC affinity chromatography is used due to its high affinity and specificity for antibodies of this class. The technique relies on the comparison of the area under the curve of the elution peak of the samples to be evaluated versus to a calibration curve of well-known concentrations and was validated by assessment of its robustness, specificity, repeatability, intermediate precision, accuracy, linearity, limit of detection, limit of quantification, and range. According to results of the study all validation parameters fulfilled the preestablished acceptance criteria and demonstrated the feasibility of the assay for the analysis of samples of cell culture supernatant as well as drug product. PMID:27379284

  10. A novel method to estimate the affinity of HLA-A∗0201 restricted CTL epitope

    NASA Astrophysics Data System (ADS)

    Xu, Yun-sheng; Lin, Yong; Zhu, Bo; Lin, Zhi-hua

    2009-02-01

    A set of 70 peptides with affinity for the class I MHC HLA-A∗0201 molecule was subjected to quantitative structure-affinity relationship studies based on the SCORE function with good results ( r2 = 0.6982, RMS = 0.280). Then the 'leave-one-out' cross-validation (LOO-CV) and an outer test set including 18 outer samples were used to validate the QSAR model. The results of the LOO-CV were q2 = 0.6188, RMS = 0.315, and the results of outer test set were r2 = 0.5633, RMS = 0.2292. All these show that the QSAR model has good predictability. Statistical analysis showed that the hydrophobic and hydrogen bond interaction played a significant role in peptide-MHC molecule binding. The study also provided useful information for structure modification of CTL epitope, and laid theoretical base for molecular design of therapeutic vaccine.

  11. Determination of binding constants by affinity capillary electrophoresis, electrospray ionization mass spectrometry and phase-distribution methods

    PubMed Central

    Chen, Zhi; Weber, Stephen G.

    2008-01-01

    Many methods for determining intermolecular interactions have been described in the literature in the past several decades. Chief among them are methods based on spectroscopic changes, particularly those based on absorption or nuclear magnetic resonance (NMR) [especially proton NMR (1H NMR)]. Recently, there have been put forward several new methods that are particularly adaptable, use very small quantities of material, and do not place severe requirements on the spectroscopic properties of the binding partners. This review covers new developments in affinity capillary electrophoresis, electrospray ionization mass spectrometry (ESI-MS) and phasetransfer methods. PMID:19802330

  12. A Novel Technique for Prealignment in Multimodality Medical Image Registration

    PubMed Central

    Zhou, Wu; Zhang, Lijuan; Xie, Yaoqin; Liang, Changhong

    2014-01-01

    Image pair is often aligned initially based on a rigid or affine transformation before a deformable registration method is applied in medical image registration. Inappropriate initial registration may compromise the registration speed or impede the convergence of the optimization algorithm. In this work, a novel technique was proposed for prealignment in both monomodality and multimodality image registration based on statistical correlation of gradient information. A simple and robust algorithm was proposed to determine the rotational differences between two images based on orientation histogram matching accumulated from local orientation of each pixel without any feature extraction. Experimental results showed that it was effective to acquire the orientation angle between two unregistered images with advantages over the existed method based on edge-map in multimodalities. Applying the orientation detection into the registration of CT/MR, T1/T2 MRI, and monomadality images with respect to rigid and nonrigid deformation improved the chances of finding the global optimization of the registration and reduced the search space of optimization. PMID:25162024

  13. Selective high-affinity polydentate ligands and methods of making such

    DOEpatents

    DeNardo, Sally; DeNardo, Gerald; Balhorn, Rodney

    2013-09-17

    This invention provides polydentate selective high affinity ligands (SHALs) that can be used in a variety of applications in a manner analogous to the use of antibodies. SHALs typically comprise a multiplicity of ligands that each binds different regions on the target molecule. The ligands are joined directly or through a linker thereby forming a polydentate moiety that typically binds the target molecule with high selectivity and avidity.

  14. Image Segmentation, Registration, Compression, and Matching

    NASA Technical Reports Server (NTRS)

    Yadegar, Jacob; Wei, Hai; Yadegar, Joseph; Ray, Nilanjan; Zabuawala, Sakina

    2011-01-01

    A novel computational framework was developed of a 2D affine invariant matching exploiting a parameter space. Named as affine invariant parameter space (AIPS), the technique can be applied to many image-processing and computer-vision problems, including image registration, template matching, and object tracking from image sequence. The AIPS is formed by the parameters in an affine combination of a set of feature points in the image plane. In cases where the entire image can be assumed to have undergone a single affine transformation, the new AIPS match metric and matching framework becomes very effective (compared with the state-of-the-art methods at the time of this reporting). No knowledge about scaling or any other transformation parameters need to be known a priori to apply the AIPS framework. An automated suite of software tools has been created to provide accurate image segmentation (for data cleaning) and high-quality 2D image and 3D surface registration (for fusing multi-resolution terrain, image, and map data). These tools are capable of supporting existing GIS toolkits already in the marketplace, and will also be usable in a stand-alone fashion. The toolkit applies novel algorithmic approaches for image segmentation, feature extraction, and registration of 2D imagery and 3D surface data, which supports first-pass, batched, fully automatic feature extraction (for segmentation), and registration. A hierarchical and adaptive approach is taken for achieving automatic feature extraction, segmentation, and registration. Surface registration is the process of aligning two (or more) data sets to a common coordinate system, during which the transformation between their different coordinate systems is determined. Also developed here are a novel, volumetric surface modeling and compression technique that provide both quality-guaranteed mesh surface approximations and compaction of the model sizes by efficiently coding the geometry and connectivity

  15. Studying primate carpal kinematics in three dimensions using a computed-tomography-based markerless registration method.

    PubMed

    Orr, Caley M; Leventhal, Evan L; Chivers, Spencer F; Marzke, Mary W; Wolfe, Scott W; Crisco, Joseph J

    2010-04-01

    The functional morphology of the wrist pertains to a number of important questions in primate evolutionary biology, including that of hominins. Reconstructing locomotor and manipulative capabilities of the wrist in extinct species requires a detailed understanding of wrist biomechanics in extant primates and the relationship between carpal form and function. The kinematics of carpal movement, and the role individual joints play in providing mobility and stability of the wrist, is central to such efforts. However, there have been few detailed biomechanical studies of the nonhuman primate wrist. This is largely because of the complexity of wrist morphology and the considerable technical challenges involved in tracking the movements of the many small bones that compose the carpus. The purpose of this article is to introduce and outline a method adapted from human clinical studies of three-dimensional (3D) carpal kinematics for use in a comparative context. The method employs computed tomography of primate cadaver forelimbs in increments throughout the wrist's range of motion, coupled with markerless registration of 3D polygon models based on inertial properties of each bone. The 3D kinematic principles involved in extracting motion axis parameters that describe bone movement are reviewed. In addition, a set of anatomically based coordinate systems embedded in the radius, capitate, hamate, lunate, and scaphoid is presented for the benefit of other primate functional morphologists interested in studying carpal kinematics. Finally, a brief demonstration of how the application of these methods can elucidate the mechanics of the wrist in primates illustrates the closer-packing of carpals in chimpanzees than in orangutans, which may help to stabilize the midcarpus and produce a more rigid wrist beneficial for efficient hand posturing during knuckle-walking locomotion. PMID:20235325

  16. African American Organ Donor Registration: A Mixed Methods Design using the Theory of Planned Behavior

    PubMed Central

    DuBay, Derek A.; Ivankova, Nataliya; Herby, Ivan; Wynn, Theresa A.; Kohler, Connie; Berry, Beverly; Foushee, Herman; Carson, April; Redden, David T.; Holt, Cheryl; Siminoff, Laura; Fouad, Mona; Martin, Michelle Y.

    2015-01-01

    Context A large racial disparity exists in organ donation. Objective The purpose of this study was to identify factors associated with becoming a registered organ donor in among African Americans in Alabama. Methods The study utilized a concurrent mixed methods design guided by the Theory of Planned Behavior to analyze African American’s decisions to become a registered organ donor using both qualitative (focus groups) and quantitative (survey) methods. Results The sample consisted of 22 registered organ donors (ROD) and 65 non-registered participants (NRP) from six focus groups completed in urban (n=3) and rural (n=3) areas. Participants emphasized the importance of the autonomy to make one’s own organ donation decision and have this decision honored posthumously. One novel barrier to becoming a ROD was the perception that organs from African Americans were often unusable due to high prevalence of chronic medical conditions such as diabetes and hypertension. Another novel theme discussed as an advantage to becoming a ROD was the subsequent motivation to take responsibility for one’s health. Family and friends were the most common groups of persons identified as approving and disapproving of the decision to become a ROD. The most common facilitator to becoming a ROD was information, while fear and the lack of information were the most common barriers. In contrast, religious beliefs, mistrust and social justice themes were infrequently referenced as barriers to becoming a ROD. Discussion Findings from this study may be useful for prioritizing organ donation community-based educational interventions in campaigns to increase donor registration. PMID:25193729

  17. Pair-wise automatic registration of three-dimensional laser scanning data from historical building by created two-dimensional images

    NASA Astrophysics Data System (ADS)

    Altuntas, Cihan

    2014-05-01

    Registration of a point cloud is a great challenge in the process of laser scanning data. So far, many registration methods have been introduced by range data, integrated camera image, and a combination of them. Moreover, the automatic registration of three-dimensional point clouds is an important research topic in both geomatics and computer sciences. In this study, keypoint-based registration of point clouds was introduced. Intensity images were created from the laser scanning data, and then a pair-wise automatic registration was performed with the keypoints extracted from the intensity images by a scale invariant feature transform (SIFT) and affine SIFT (ASIFT). The results were compared with the iterative closest point, which has high accuracy and is the extensively adopted method for the pair-wise registration. Consequently, SIFT and ASIFT keypoints which were extracted from intensity images can be exploited to pair-wise automatic registration of the point clouds.

  18. Evaluation of five non-rigid image registration algorithms using the NIREP framework

    NASA Astrophysics Data System (ADS)

    Wei, Ying; Christensen, Gary E.; Song, Joo Hyun; Rudrauf, David; Bruss, Joel; Kuhl, Jon G.; Grabowski, Thomas J.

    2010-03-01

    Evaluating non-rigid image registration algorithm performance is a difficult problem since there is rarely a "gold standard" (i.e., known) correspondence between two images. This paper reports the analysis and comparison of five non-rigid image registration algorithms using the Non-Rigid Image Registration Evaluation Project (NIREP) (www.nirep.org) framework. The NIREP framework evaluates registration performance using centralized databases of well-characterized images and standard evaluation statistics (methods) which are implemented in a software package. The performance of five non-rigid registration algorithms (Affine, AIR, Demons, SLE and SICLE) was evaluated using 22 images from two NIREP neuroanatomical evaluation databases. Six evaluation statistics (relative overlap, intensity variance, normalized ROI overlap, alignment of calcarine sulci, inverse consistency error and transitivity error) were used to evaluate and compare image registration performance. The results indicate that the Demons registration algorithm produced the best registration results with respect to the relative overlap statistic but produced nearly the worst registration results with respect to the inverse consistency statistic. The fact that one registration algorithm produced the best result for one criterion and nearly the worst for another illustrates the need to use multiple evaluation statistics to fully assess performance.

  19. Quantitative evaluation of image registration techniques in the case of retinal images

    NASA Astrophysics Data System (ADS)

    Gavet, Yann; Fernandes, Mathieu; Pinoli, Jean-Charles

    2012-04-01

    In human retina observation (with non mydriatic optical microscopes), an image registration process is often employed to enlarge the field of view. Analyzing all the images takes a lot of time. Numerous techniques have been proposed to perform the registration process. Its good evaluation is a difficult question that is then raising. This article presents the use of two quantitative criterions to evaluate and compare some classical feature-based image registration techniques. The images are first segmented and the resulting binary images are then registered. The good quality of the registration process is evaluated with a normalized criterion based on the ɛ dissimilarity criterion, and the figure of merit criterion (fom), for 25 pairs of images with a manual selection of control points. These criterions are normalized by the results of the affine method (considered as the most simple method). Then, for each pair, the influence of the number of points used to perform the registration is evaluated.

  20. Affinity Chromatography.

    ERIC Educational Resources Information Center

    Gray, Gary R.

    1980-01-01

    Presents selected recent advances in immobilization chemistry which have important connections to affinity chromatography. Discusses ligand immobilization and support modification. Cites 51 references. (CS)

  1. Multi-modal robust inverse-consistent linear registration.

    PubMed

    Wachinger, Christian; Golland, Polina; Magnain, Caroline; Fischl, Bruce; Reuter, Martin

    2015-04-01

    Registration performance can significantly deteriorate when image regions do not comply with model assumptions. Robust estimation improves registration accuracy by reducing or ignoring the contribution of voxels with large intensity differences, but existing approaches are limited to monomodal registration. In this work, we propose a robust and inverse-consistent technique for cross-modal, affine image registration. The algorithm is derived from a contextual framework of image registration. The key idea is to use a modality invariant representation of images based on local entropy estimation, and to incorporate a heteroskedastic noise model. This noise model allows us to draw the analogy to iteratively reweighted least squares estimation and to leverage existing weighting functions to account for differences in local information content in multimodal registration. Furthermore, we use the nonparametric windows density estimator to reliably calculate entropy of small image patches. Finally, we derive the Gauss-Newton update and show that it is equivalent to the efficient second-order minimization for the fully symmetric registration approach. We illustrate excellent performance of the proposed methods on datasets containing outliers for alignment of brain tumor, full head, and histology images. PMID:25470798

  2. Multi-Modal Robust Inverse-Consistent Linear Registration

    PubMed Central

    Wachinger, Christian; Golland, Polina; Magnain, Caroline; Fischl, Bruce; Reuter, Martin

    2016-01-01

    Registration performance can significantly deteriorate when image regions do not comply with model assumptions. Robust estimation improves registration accuracy by reducing or ignoring the contribution of voxels with large intensity differences, but existing approaches are limited to monomodal registration. In this work, we propose a robust and inverse-consistent technique for crossmodal, affine image registration. The algorithm is derived from a contextual framework of image registration. The key idea is to use a modality invariant representation of images based on local entropy estimation, and to incorporate a heteroskedastic noise model. This noise model allows us to draw the analogy to iteratively reweighted least squares estimation and to leverage existing weighting functions to account for differences in local information content in multimodal registration. Furthermore, we use the nonparametric windows density estimator to reliably calculate entropy of small image patches. Finally, we derive the Gauss–Newton update and show that it is equivalent to the efficient secondorder minimization for the fully symmetric registration approach. We illustrate excellent performance of the proposed methods on datasets containing outliers for alignment of brain tumor, full head, and histology images. PMID:25470798

  3. Student Engagement and Course Registration Methods as Possible Predictors of Freshman Retention

    ERIC Educational Resources Information Center

    Bass, Laura H.; Ballard, Angela S.

    2012-01-01

    A study by Kenney, Kenney, and Dumont (2005) identified a supportive learning environment as one of the five indicators for collegiate student engagement, a concept that extends beyond the classroom to permeate the entire educational environment. A student's level of engagement can be impacted as early as orientation and registration, when he is…

  4. An automated, fast and accurate registration method to link stranded seeds in permanent prostate implants.

    PubMed

    Westendorp, Hendrik; Nuver, Tonnis T; Moerland, Marinus A; Minken, André W

    2015-10-21

    The geometry of a permanent prostate implant varies over time. Seeds can migrate and edema of the prostate affects the position of seeds. Seed movements directly influence dosimetry which relates to treatment quality. We present a method that tracks all individual seeds over time allowing quantification of seed movements. This linking procedure was tested on transrectal ultrasound (TRUS) and cone-beam CT (CBCT) datasets of 699 patients. These datasets were acquired intraoperatively during a dynamic implantation procedure, that combines both imaging modalities. The procedure was subdivided in four automatic linking steps. (I) The Hungarian Algorithm was applied to initially link seeds in CBCT and the corresponding TRUS datasets. (II) Strands were identified and optimized based on curvature and linefits: non optimal links were removed. (III) The positions of unlinked seeds were reviewed and were linked to incomplete strands if within curvature- and distance-thresholds. (IV) Finally, seeds close to strands were linked, also if the curvature-threshold was violated. After linking the seeds an affine transformation was applied. The procedure was repeated until the results were stable or the 6th iteration ended. All results were visually reviewed for mismatches and uncertainties. Eleven implants showed a mismatch and in 12 cases an uncertainty was identified. On average the linking procedure took 42 ms per case. This accurate and fast method has the potential to be used for other time spans, like Day 30, and other imaging modalities. It can potentially be used during a dynamic implantation procedure to faster and better evaluate the quality of the permanent prostate implant. PMID:26439900

  5. An automated, fast and accurate registration method to link stranded seeds in permanent prostate implants

    NASA Astrophysics Data System (ADS)

    Westendorp, Hendrik; Nuver, Tonnis T.; Moerland, Marinus A.; Minken, André W.

    2015-10-01

    The geometry of a permanent prostate implant varies over time. Seeds can migrate and edema of the prostate affects the position of seeds. Seed movements directly influence dosimetry which relates to treatment quality. We present a method that tracks all individual seeds over time allowing quantification of seed movements. This linking procedure was tested on transrectal ultrasound (TRUS) and cone-beam CT (CBCT) datasets of 699 patients. These datasets were acquired intraoperatively during a dynamic implantation procedure, that combines both imaging modalities. The procedure was subdivided in four automatic linking steps. (I) The Hungarian Algorithm was applied to initially link seeds in CBCT and the corresponding TRUS datasets. (II) Strands were identified and optimized based on curvature and linefits: non optimal links were removed. (III) The positions of unlinked seeds were reviewed and were linked to incomplete strands if within curvature- and distance-thresholds. (IV) Finally, seeds close to strands were linked, also if the curvature-threshold was violated. After linking the seeds an affine transformation was applied. The procedure was repeated until the results were stable or the 6th iteration ended. All results were visually reviewed for mismatches and uncertainties. Eleven implants showed a mismatch and in 12 cases an uncertainty was identified. On average the linking procedure took 42 ms per case. This accurate and fast method has the potential to be used for other time spans, like Day 30, and other imaging modalities. It can potentially be used during a dynamic implantation procedure to faster and better evaluate the quality of the permanent prostate implant.

  6. Non-rigid registration of small animal skeletons from micro-CT using 3D shape context

    NASA Astrophysics Data System (ADS)

    Xiao, Di; Bourgeat, Pierrick; Fripp, Jurgen; Acosta Tamayo, Oscar; Gregoire, Marie Claude; Salvado, Olivier

    2009-02-01

    Small animal registration is an important step for molecular image analysis. Skeleton registration from whole-body or only partial micro Computerized Tomography (CT) image is often performed to match individual rats to atlases and templates, for example to identify organs in positron emission tomography (PET). In this paper, we extend the shape context matching technique for 3D surface registration and apply it for rat hind limb skeleton registration from CT images. Using the proposed method, after standard affine iterative closest point (ICP) registration, correspondences between the 3D points from sour and target objects were robustly found and used to deform the limb skeleton surface with thin-plate-spline (TPS). Experiments are described using phantoms and actual rat hind limb skeletons. On animals, mean square errors were decreased by the proposed registration compared to that of its initial alignment. Visually, skeletons were successfully registered even in cases of very different animal poses.

  7. Voter Registration and Canvassing.

    ERIC Educational Resources Information Center

    Institute for Political/Legal Education, Sewell, NJ.

    Detailed procedures for community voter registration surveys to be conducted by high school students are presented. Methods for organizational structure, selection of canvassing districts, conducting the survey, processing the data, and initiating a registration drive are outlined. Student personnel include a general coordinator, a field staff to…

  8. Fast voxel-based 2D/3D registration algorithm using a volume rendering method based on the shear-warp factorization

    NASA Astrophysics Data System (ADS)

    Weese, Juergen; Goecke, Roland; Penney, Graeme P.; Desmedt, Paul; Buzug, Thorsten M.; Schumann, Heidrun

    1999-05-01

    2D/3D registration makes it possible to use pre-operative CT scans for navigation purposes during X-ray fluoroscopy guided interventions. We present a fast voxel-based method for this registration task, which uses a recently introduced similarity measure (pattern intensity). This measure is especially suitable for 2D/3D registration, because it is robust with respect to structures such as a stent visible in the X-ray fluoroscopy image but not in the CT scan. The method uses only a part of the CT scan for the generation of digitally reconstructed radiographs (DRRs) to accelerate their computation. Nevertheless, computation time is crucial for intra-operative application and a further speed-up is required, because numerous DRRs must be computed. For that reason, the suitability of different volume rendering methods for 2D/3D registration has been investigated. A method based on the shear-warp factorization of the viewing transformation turned out to be especially suitable and builds the basis of the registration algorithm. The algorithm has been applied to images of a spine phantom and to clinical images. For comparison, registration results have been calculated using ray-casting. The shear-warp factorization based rendering method accelerates registration by a factor of up to seven compared to ray-casting without degrading registration accuracy. Using a vertebra as feature for registration, computation time is in the range of 3-4s (Sun UltraSparc, 300 MHz) which is acceptable for intra-operative application.

  9. DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

    PubMed Central

    Rajeev, Lara; Luning, Eric G.; Mukhopadhyay, Aindrila

    2014-01-01

    In vivo methods such as ChIP-chip are well-established techniques used to determine global gene targets for transcription factors. However, they are of limited use in exploring bacterial two component regulatory systems with uncharacterized activation conditions. Such systems regulate transcription only when activated in the presence of unique signals. Since these signals are often unknown, the in vitro microarray based method described in this video article can be used to determine gene targets and binding sites for response regulators. This DNA-affinity-purified-chip method may be used for any purified regulator in any organism with a sequenced genome. The protocol involves allowing the purified tagged protein to bind to sheared genomic DNA and then affinity purifying the protein-bound DNA, followed by fluorescent labeling of the DNA and hybridization to a custom tiling array. Preceding steps that may be used to optimize the assay for specific regulators are also described. The peaks generated by the array data analysis are used to predict binding site motifs, which are then experimentally validated. The motif predictions can be further used to determine gene targets of orthologous response regulators in closely related species. We demonstrate the applicability of this method by determining the gene targets and binding site motifs and thus predicting the function for a sigma54-dependent response regulator DVU3023 in the environmental bacterium Desulfovibrio vulgaris Hildenborough. PMID:25079303

  10. A Simple Three-Step Method for Design and Affinity Testing of New Antisense Peptides: An Example of Erythropoietin

    PubMed Central

    Štambuk, Nikola; Manojlović, Zoran; Turčić, Petra; Martinić, Roko; Konjevoda, Paško; Weitner, Tin; Wardega, Piotr; Gabričević, Mario

    2014-01-01

    Antisense peptide technology is a valuable tool for deriving new biologically active molecules and performing peptide–receptor modulation. It is based on the fact that peptides specified by the complementary (antisense) nucleotide sequences often bind to each other with a higher specificity and efficacy. We tested the validity of this concept on the example of human erythropoietin, a well-characterized and pharmacologically relevant hematopoietic growth factor. The purpose of the work was to present and test simple and efficient three-step procedure for the design of an antisense peptide targeting receptor-binding site of human erythropoietin. Firstly, we selected the carboxyl-terminal receptor binding region of the molecule (epitope) as a template for the antisense peptide modeling; Secondly, we designed an antisense peptide using mRNA transcription of the epitope sequence in the 3'→5' direction and computational screening of potential paratope structures with BLAST; Thirdly, we evaluated sense–antisense (epitope–paratope) peptide binding and affinity by means of fluorescence spectroscopy and microscale thermophoresis. Both methods showed similar Kd values of 850 and 816 µM, respectively. The advantages of the methods were: fast screening with a small quantity of the sample needed, and measurements done within the range of physicochemical parameters resembling physiological conditions. Antisense peptides targeting specific erythropoietin region(s) could be used for the development of new immunochemical methods. Selected antisense peptides with optimal affinity are potential lead compounds for the development of novel diagnostic substances, biopharmaceuticals and vaccines. PMID:24865486

  11. A simple three-step method for design and affinity testing of new antisense peptides: an example of erythropoietin.

    PubMed

    Štambuk, Nikola; Manojlović, Zoran; Turčić, Petra; Martinić, Roko; Konjevoda, Paško; Weitner, Tin; Wardega, Piotr; Gabričević, Mario

    2014-01-01

    Antisense peptide technology is a valuable tool for deriving new biologically active molecules and performing peptide-receptor modulation. It is based on the fact that peptides specified by the complementary (antisense) nucleotide sequences often bind to each other with a higher specificity and efficacy. We tested the validity of this concept on the example of human erythropoietin, a well-characterized and pharmacologically relevant hematopoietic growth factor. The purpose of the work was to present and test simple and efficient three-step procedure for the design of an antisense peptide targeting receptor-binding site of human erythropoietin. Firstly, we selected the carboxyl-terminal receptor binding region of the molecule (epitope) as a template for the antisense peptide modeling; Secondly, we designed an antisense peptide using mRNA transcription of the epitope sequence in the 3'→5' direction and computational screening of potential paratope structures with BLAST; Thirdly, we evaluated sense-antisense (epitope-paratope) peptide binding and affinity by means of fluorescence spectroscopy and microscale thermophoresis. Both methods showed similar Kd values of 850 and 816 µM, respectively. The advantages of the methods were: fast screening with a small quantity of the sample needed, and measurements done within the range of physicochemical parameters resembling physiological conditions. Antisense peptides targeting specific erythropoietin region(s) could be used for the development of new immunochemical methods. Selected antisense peptides with optimal affinity are potential lead compounds for the development of novel diagnostic substances, biopharmaceuticals and vaccines. PMID:24865486

  12. [Development of Selective LC Analysis Method for Biogenic and Related Compounds Based on a Fluorous Affinity Technique].

    PubMed

    Hayama, Tadashi

    2015-01-01

    A separation-oriented derivatization method combined with LC has been developed for the selective analysis of biogenic and related compounds. In this method, we utilized a specific affinity between perfluoroalkyl-containing compounds, i.e., 'fluorous' compounds (fluorophilicity). Our strategy involves the derivatization of target analytes with perfluoroalkyl reagents, followed by selective retention of the derivatives with a perfluoroalkyl-modified stationary phase LC column. The perfluoroalkylated derivatives are strongly retained on the column owing to their fluorophilicity, whereas non-derivatized species, such as sample matrices, are hardly retained. Therefore, utilizing this derivatization method, target analytes can be determined selectively without interference from matrices. This method has been successfully applied to the LC analysis of some biogenic and related compounds in complex biological samples. PMID:26329550

  13. Motion tracking in the liver: Validation of a method based on 4D ultrasound using a nonrigid registration technique

    SciTech Connect

    Vijayan, Sinara; Klein, Stefan; Hofstad, Erlend Fagertun; Langø, Thomas; Lindseth, Frank; Ystgaard, Brynjulf

    2014-08-15

    Purpose: Treatments like radiotherapy and focused ultrasound in the abdomen require accurate motion tracking, in order to optimize dosage delivery to the target and minimize damage to critical structures and healthy tissues around the target. 4D ultrasound is a promising modality for motion tracking during such treatments. In this study, the authors evaluate the accuracy of motion tracking in the liver based on deformable registration of 4D ultrasound images. Methods: The offline analysis was performed using a nonrigid registration algorithm that was specifically designed for motion estimation from dynamic imaging data. The method registers the entire 4D image data sequence in a groupwise optimization fashion, thus avoiding a bias toward a specifically chosen reference time point. Three healthy volunteers were scanned over several breathing cycles (12 s) from three different positions and angles on the abdomen; a total of nine 4D scans for the three volunteers. Well-defined anatomic landmarks were manually annotated in all 96 time frames for assessment of the automatic algorithm. The error of the automatic motion estimation method was compared with interobserver variability. The authors also performed experiments to investigate the influence of parameters defining the deformation field flexibility and evaluated how well the method performed with a lower temporal resolution in order to establish the minimum frame rate required for accurate motion estimation. Results: The registration method estimated liver motion with an error of 1 mm (75% percentile over all datasets), which was lower than the interobserver variability of 1.4 mm. The results were only slightly dependent on the degrees of freedom of the deformation model. The registration error increased to 2.8 mm with an eight times lower temporal resolution. Conclusions: The authors conclude that the methodology was able to accurately track the motion of the liver in the 4D ultrasound data. The authors believe

  14. Dual affinity method for plasmid DNA purification in aqueous two-phase systems.

    PubMed

    Barbosa, H S C; Hine, A V; Brocchini, S; Slater, N K H; Marcos, J C

    2010-02-26

    The DNA binding fusion protein, LacI-His6-GFP, together with the conjugate PEG-IDA-Cu(II) (10 kDa) was evaluated as a dual affinity system for the pUC19 plasmid extraction from an alkaline bacterial cell lysate in poly(ethylene glycol) (PEG)/dextran (DEX) aqueous two-phase systems (ATPS). In a PEG 600-DEX 40 ATPS containing 0.273 nmol of LacI fusion protein and 0.14% (w/w) of the functionalised PEG-IDA-Cu(II), more than 72% of the plasmid DNA partitioned to the PEG phase, without RNA or genomic DNA contamination as evaluated by agarose gel electrophoresis. In a second extraction stage, the elution of pDNA from the LacI binding complex proved difficult using either dextran or phosphate buffer as second phase, though more than 75% of the overall protein was removed in both systems. A maximum recovery of approximately 27% of the pCU19 plasmid was achieved using the PEG-dextran system as a second extraction system, with 80-90% of pDNA partitioning to the bottom phase. This represents about 7.4 microg of pDNA extracted per 1 mL of pUC19 desalted lysate. PMID:20083249

  15. Rapid contrast evaluation method based on affinity beads and backscattered electron imaging for the screening of electron stains.

    PubMed

    Kaku, Hiroki; Inoue, Kanako; Muranaka, Yoshinori; Park, Pyoyun; Ikeda, Kenichi

    2015-10-01

    Uranyl salts are toxic and radioactive; therefore, several studies have been conducted to screen for substitutes of electron stains. In this regard, the contrast evaluation process is time consuming and the results obtained are inconsistent. In this study, we developed a novel contrast evaluation method using affinity beads and a backscattered electron image (BSEI), obtained using scanning electron microscopy. The contrast ratios of BSEI in each electron stain treatment were correlated with those of transmission electron microscopic images. The affinity beads bound to cell components independently. Protein and DNA samples were enhanced by image contrast treated with electron stains; however, this was not observed for sugars. Protein-conjugated beads showed an additive effect of image contrast when double-stained with lead. However, additive effect of double staining was not observed in DNA-conjugated beads. The varying chemical properties of oligopeptides showed differences in image contrast when treated with each electron stain. This BSEI-based evaluation method not only enables screening for alternate electron stains, but also helps analyze the underlying mechanisms of electron staining of cellular structures. PMID:26199255

  16. A non-rigid registration method for cerebral DSA images based on forward and inverse stretching - avoiding bilinear interpolation.

    PubMed

    Liu, Bin; Zhang, Bingbing; Wan, Chao; Dong, Yihuan

    2014-01-01

    In order to reduce the motion artifact caused by the patient in cerebral DSA images, a non-rigid registration method based on stretching transformation is presented in this paper. Unlike other traditional methods, it does not need bilinear interpolation which is rather time-consuming and even produce 'originally non-existent gray value'. By this method, the mask image is rasterized to generate appropriate control points. The Energy of Histogram of Differences criterion is adopted as similarity measurement, and the Powell algorithm is utilized for acceleration. A forward stretching transformation is used to complete motion estimation and an inverse stretching transformation to generate target image by pixel mapping strategy. This method is effective to maintain the topological relationships of the gray value before and after the image deformation. The mask image remains clear and accurate contours, and the quality of the subtraction image after the registration is favorable. This method can provide support for clinical treatment and diagnosis of cerebral disease. PMID:24212008

  17. Feature-Based Registration Techniques

    NASA Astrophysics Data System (ADS)

    Lorenz, Cristian; Klinder, Tobias; von Berg, Jens

    In contrast to intensity-based image registration, where a similarity measure is typically evaluated at each voxel location, feature-based registration works on a sparse set of image locations. Therefore, it needs an explicit step of interpolation to supply a dense deformation field. In this chapter, the application of feature-based registration to pulmonary image registration as well as hybrid methods, combining feature-based with intensity-based registration, is discussed. In contrast to pure feature based registration methods, hybrid methods are increasingly proposed in the pulmonary context and have the potential to out-perform purely intensity based registration methods. Available approaches will be classified along the categories feature type, correspondence definition, and interpolation type to finally achieve a dense deformation field.

  18. An accuracy assessment of different rigid body image registration methods and robotic couch positional corrections using a novel phantom

    SciTech Connect

    Arumugam, Sankar; Xing Aitang; Jameson, Michael G.; Holloway, Lois

    2013-03-15

    Purpose: Image guided radiotherapy (IGRT) using cone beam computed tomography (CBCT) images greatly reduces interfractional patient positional uncertainties. An understanding of uncertainties in the IGRT process itself is essential to ensure appropriate use of this technology. The purpose of this study was to develop a phantom capable of assessing the accuracy of IGRT hardware and software including a 6 degrees of freedom patient positioning system and to investigate the accuracy of the Elekta XVI system in combination with the HexaPOD robotic treatment couch top. Methods: The constructed phantom enabled verification of the three automatic rigid body registrations (gray value, bone, seed) available in the Elekta XVI software and includes an adjustable mount that introduces known rotational offsets to the phantom from its reference position. Repeated positioning of the phantom was undertaken to assess phantom rotational accuracy. Using this phantom the accuracy of the XVI registration algorithms was assessed considering CBCT hardware factors and image resolution together with the residual error in the overall image guidance process when positional corrections were performed through the HexaPOD couch system. Results: The phantom positioning was found to be within 0.04 ({sigma}= 0.12) Degree-Sign , 0.02 ({sigma}= 0.13) Degree-Sign , and -0.03 ({sigma}= 0.06) Degree-Sign in X, Y, and Z directions, respectively, enabling assessment of IGRT with a 6 degrees of freedom patient positioning system. The gray value registration algorithm showed the least error in calculated offsets with maximum mean difference of -0.2({sigma}= 0.4) mm in translational and -0.1({sigma}= 0.1) Degree-Sign in rotational directions for all image resolutions. Bone and seed registration were found to be sensitive to CBCT image resolution. Seed registration was found to be most sensitive demonstrating a maximum mean error of -0.3({sigma}= 0.9) mm and -1.4({sigma}= 1.7) Degree-Sign in translational

  19. A fast rigid-registration method of inferior limb X-ray image and 3D CT images for TKA surgery

    NASA Astrophysics Data System (ADS)

    Ito, Fumihito; O. D. A, Prima; Uwano, Ikuko; Ito, Kenzo

    2010-03-01

    In this paper, we propose a fast rigid-registration method of inferior limb X-ray films (two-dimensional Computed Radiography (CR) images) and three-dimensional Computed Tomography (CT) images for Total Knee Arthroplasty (TKA) surgery planning. The position of the each bone, such as femur and tibia (shin bone), in X-ray film and 3D CT images is slightly different, and we must pay attention how to use the two different images, since X-ray film image is captured in the standing position, and 3D CT is captured in decubitus (face up) position, respectively. Though the conventional registration mainly uses cross-correlation function between two images,and utilizes optimization techniques, it takes enormous calculation time and it is difficult to use it in interactive operations. In order to solve these problems, we calculate the center line (bone axis) of femur and tibia (shin bone) automatically, and we use them as initial positions for the registration. We evaluate our registration method by using three patient's image data, and we compare our proposed method and a conventional registration, which uses down-hill simplex algorithm. The down-hill simplex method is an optimization algorithm that requires only function evaluations, and doesn't need the calculation of derivatives. Our registration method is more effective than the downhill simplex method in computational time and the stable convergence. We have developed the implant simulation system on a personal computer, in order to support the surgeon in a preoperative planning of TKA. Our registration method is implemented in the simulation system, and user can manipulate 2D/3D translucent templates of implant components on X-ray film and 3D CT images.

  20. Compositions and methods comprising cellulase variants with reduced affinity to non-cellulosic materials

    SciTech Connect

    Cascao-Pereira, Luis G; Kaper, Thijs; Kelemen, Bradley R; Liu, Amy D

    2015-04-07

    The present disclosure relates to cellulase variants. In particular the present disclosure relates to cellulase variants having reduced binding to non-cellulosic materials. Also described are nucleic acids encoding the cellulase, compositions comprising said cellulase, methods of identifying cellulose variants and methods of using the compositions.

  1. A novel molecularly imprinted method with computational simulation for the affinity isolation and knockout of baicalein from Scutellaria baicalensis.

    PubMed

    Li, Hong; He, Hongliang; Huang, Jiaojiao; Wang, Chong-Zhi; Gu, Xiaoli; Gao, Yankun; Zhang, Hongjuan; Du, Shuhu; Chen, Lina; Yuan, Chun-Su

    2016-02-01

    A novel molecularly imprinted polymer (MIP) was synthesized by precipitation polymerization with baicalein (BAI) as the template and used as solid-phase extraction (SPE) adsorbent, aiming at the affinity isolation and selective knockout of BAI from Scutellaria baicalensis Georgi (SB). We used computational simulation to predict the optimal functional monomer, polymerization solvent and molar ratio of template to functional monomer. Characterization and performance tests revealed that MIP exhibited uniform spherical morphology, rapid binding kinetics, and higher adsorption capacity for BAI compared with nonimprinted polymer (NIP). The application of MIP in SPE coupled with high-performance liquid chromatography to extract BAI from SB showed excellent recovery (94.3%) and purity (97.0%). Not only the single BAI compound, but also the BAI-removed SB extract was obtained by one-step process. This new method is useful for isolation and knockout of key bioactive compounds from herbal medicines. PMID:26037609

  2. Image registration with uncertainty analysis

    DOEpatents

    Simonson, Katherine M.

    2011-03-22

    In an image registration method, edges are detected in a first image and a second image. A percentage of edge pixels in a subset of the second image that are also edges in the first image shifted by a translation is calculated. A best registration point is calculated based on a maximum percentage of edges matched. In a predefined search region, all registration points other than the best registration point are identified that are not significantly worse than the best registration point according to a predetermined statistical criterion.

  3. SU-E-J-58: Comparison of Conformal Tracking Methods Using Initial, Adaptive and Preceding Image Frames for Image Registration

    SciTech Connect

    Teo, P; Guo, K; Alayoubi, N; Kehler, K; Pistorius, S

    2015-06-15

    Purpose: Accounting for tumor motion during radiation therapy is important to ensure that the tumor receives the prescribed dose. Increasing the field size to account for this motion exposes the surrounding healthy tissues to unnecessary radiation. In contrast to using motion-encompassing techniques to treat moving tumors, conformal radiation therapy (RT) uses a smaller field to track the tumor and adapts the beam aperture according to the motion detected. This work investigates and compares the performance of three markerless, EPID based, optical flow methods to track tumor motion with conformal RT. Methods: Three techniques were used to track the motions of a 3D printed lung tumor programmed to move according to the tumor of seven lung cancer patients. These techniques utilized a multi-resolution optical flow algorithm as the core computation for image registration. The first method (DIR) registers the incoming images with an initial reference frame, while the second method (RFSF) uses an adaptive reference frame and the third method (CU) uses preceding image frames for registration. The patient traces and errors were evaluated for the seven patients. Results: The average position errors for all patient traces were 0.12 ± 0.33 mm, −0.05 ± 0.04 mm and −0.28 ± 0.44 mm for CU, DIR and RFSF method respectively. The position errors distributed within 1 standard deviation are 0.74 mm, 0.37 mm and 0.96 mm respectively. The CU and RFSF algorithms are sensitive to the characteristics of the patient trace and produce a wider distribution of errors amongst patients. Although the mean error for the DIR method is negatively biased (−0.05 mm) for all patients, it has the narrowest distribution of position error, which can be corrected using an offset calibration. Conclusion: Three techniques of image registration and position update were studied. Using direct comparison with an initial frame yields the best performance. The authors would like to thank Dr.YeLin Suh for

  4. A method of 2D/3D registration of a statistical mouse atlas with a planar X-ray projection and an optical photo

    PubMed Central

    Wang, Hongkai; Stout, David B; Chatziioannou, Arion F

    2013-01-01

    The development of sophisticated and high throughput whole body small animal imaging technologies has created a need for improved image analysis and increased automation. The registration of a digital mouse atlas to individual images is a prerequisite for automated organ segmentation and uptake quantification. This paper presents a fully-automatic method for registering a statistical mouse atlas with individual subjects based on an anterior-posterior X-ray projection and a lateral optical photo of the mouse silhouette. The mouse atlas was trained as a statistical shape model based on 83 organ-segmented micro-CT images. For registration, a hierarchical approach is applied which first registers high contrast organs, and then estimates low contrast organs based on the registered high contrast organs. To register the high contrast organs, a 2D-registration-back-projection strategy is used that deforms the 3D atlas based on the 2D registrations of the atlas projections. For validation, this method was evaluated using 55 subjects of preclinical mouse studies. The results showed that this method can compensate for moderate variations of animal postures and organ anatomy. Two different metrics, the Dice coefficient and the average surface distance, were used to assess the registration accuracy of major organs. The Dice coefficients vary from 0.31±0.16 for the spleen to 0.88±0.03 for the whole body, and the average surface distance varies from 0.54±0.06 mm for the lungs to 0.85±0.10 mm for the skin. The method was compared with a direct 3D deformation optimization (without 2D-registration-back-projection) and a single-subject atlas registration (instead of using the statistical atlas). The comparison revealed that the 2D-registration-back-projection strategy significantly improved the registration accuracy, and the use of the statistical mouse atlas led to more plausible organ shapes than the single-subject atlas. This method was also tested with shoulder xenograft

  5. Assessment of Thematic Mapper Band-to-band Registration by the Block Correlation Method

    NASA Technical Reports Server (NTRS)

    Card, D. H.; Wrigley, R. C.; Mertz, F. C.; Hall, J. R.

    1985-01-01

    Rectangular blocks of pixels from one band image were statistically correlated against blocks centered on identical pixels from a second band image. The block pairs were shifted in pixel increments both vertically and horizontally with respect to each other and the correlation coefficient to the maximum correlation was taken as the best estimate of registration error for each block pair. For the band combinations of the Arkansas scene studied, the misregistration of TM spectral bands within the noncooled focal plane lie well within the 0.2 pixel target specification. Misregistration between the middle IR bands is well within this specification also. The thermal IR band has an apparent misregistration with TM band 7 of approximately 3 pixels in each direction. The TM band 3 has a misregistration of approximately 0.2 pixel in the across-scan direction and 0.5 pixel in the along-scan direction, with both TM bands 5 and 7.

  6. Assessment of Thematic Mapper band-to-band registration by the block correlation method

    NASA Technical Reports Server (NTRS)

    Card, D. H.; Wrigley, R. C.; Mertz, F. C.; Hall, J. R.

    1983-01-01

    Rectangular blocks of pixels from one band image were statistically correlated against blocks centered on identical pixels from a second band image. The block pairs were shifted in pixel increments both vertically and horizontally with respect to each other and the correlation coefficient to the maximum correlation was taken as the best estimate of registration error for each block pair. For the band combinations of the Arkansas scene studied, the misregistration of TM spectral bands within the noncooled focal plane lie well within the 0.2 pixel target specification. Misregistration between the middle IR bands is well within this specification also. The thermal IR band has an apparent misregistration with TM band 7 of approximately 3 pixels in each direction. The TM band 3 has a misregistration of approximately 0.2 pixel in the across-scan direction and 0.5 pixel in the along-scan direction, with both TM bands 5 and 7.

  7. Fast Modeling of Binding Affinities by Means of Superposing Significant Interaction Rules (SSIR) Method.

    PubMed

    Besalú, Emili

    2016-01-01

    The Superposing Significant Interaction Rules (SSIR) method is described. It is a general combinatorial and symbolic procedure able to rank compounds belonging to combinatorial analogue series. The procedure generates structure-activity relationship (SAR) models and also serves as an inverse SAR tool. The method is fast and can deal with large databases. SSIR operates from statistical significances calculated from the available library of compounds and according to the previously attached molecular labels of interest or non-interest. The required symbolic codification allows dealing with almost any combinatorial data set, even in a confidential manner, if desired. The application example categorizes molecules as binding or non-binding, and consensus ranking SAR models are generated from training and two distinct cross-validation methods: leave-one-out and balanced leave-two-out (BL2O), the latter being suited for the treatment of binary properties. PMID:27240346

  8. Fast Modeling of Binding Affinities by Means of Superposing Significant Interaction Rules (SSIR) Method

    PubMed Central

    Besalú, Emili

    2016-01-01

    The Superposing Significant Interaction Rules (SSIR) method is described. It is a general combinatorial and symbolic procedure able to rank compounds belonging to combinatorial analogue series. The procedure generates structure-activity relationship (SAR) models and also serves as an inverse SAR tool. The method is fast and can deal with large databases. SSIR operates from statistical significances calculated from the available library of compounds and according to the previously attached molecular labels of interest or non-interest. The required symbolic codification allows dealing with almost any combinatorial data set, even in a confidential manner, if desired. The application example categorizes molecules as binding or non-binding, and consensus ranking SAR models are generated from training and two distinct cross-validation methods: leave-one-out and balanced leave-two-out (BL2O), the latter being suited for the treatment of binary properties. PMID:27240346

  9. A multiple-image-based method to evaluate the performance of deformable image registration in the pelvis

    NASA Astrophysics Data System (ADS)

    Saleh, Ziad; Thor, Maria; Apte, Aditya P.; Sharp, Gregory; Tang, Xiaoli; Veeraraghavan, Harini; Muren, Ludvig; Deasy, Joseph

    2016-08-01

    Deformable image registration (DIR) is essential for adaptive radiotherapy (RT) for tumor sites subject to motion, changes in tumor volume, as well as changes in patient normal anatomy due to weight loss. Several methods have been published to evaluate DIR-related uncertainties but they are not widely adopted. The aim of this study was, therefore, to evaluate intra-patient DIR for two highly deformable organs—the bladder and the rectum—in prostate cancer RT using a quantitative metric based on multiple image registration, the distance discordance metric (DDM). Voxel-by-voxel DIR uncertainties of the bladder and rectum were evaluated using DDM on weekly CT scans of 38 subjects previously treated with RT for prostate cancer (six scans/subject). The DDM was obtained from group-wise B-spline registration of each patient’s collection of repeat CT scans. For each structure, registration uncertainties were derived from DDM-related metrics. In addition, five other quantitative measures, including inverse consistency error (ICE), transitivity error (TE), Dice similarity (DSC) and volume ratios between corresponding structures from pre- and post- registered images were computed and compared with the DDM. The DDM varied across subjects and structures; DDMmean of the bladder ranged from 2 to 13 mm and from 1 to 11 mm for the rectum. There was a high correlation between DDMmean of the bladder and the rectum (Pearson’s correlation coefficient, R p  =  0.62). The correlation between DDMmean and the volume ratios post-DIR was stronger (R p  =  0.51 0.68) than the correlation with the TE (bladder: R p  =  0.46 rectum: R p  =  0.47), or the ICE (bladder: R p  =  0.34 rectum: R p  =  0.37). There was a negative correlation between DSC and DDMmean of both the bladder (R p  =  ‑0.23) and the rectum (R p  =  ‑0.63). The DDM uncertainty metric indicated considerable DIR variability across subjects and

  10. A multiple-image-based method to evaluate the performance of deformable image registration in the pelvis.

    PubMed

    Saleh, Ziad; Thor, Maria; Apte, Aditya P; Sharp, Gregory; Tang, Xiaoli; Veeraraghavan, Harini; Muren, Ludvig; Deasy, Joseph

    2016-08-21

    Deformable image registration (DIR) is essential for adaptive radiotherapy (RT) for tumor sites subject to motion, changes in tumor volume, as well as changes in patient normal anatomy due to weight loss. Several methods have been published to evaluate DIR-related uncertainties but they are not widely adopted. The aim of this study was, therefore, to evaluate intra-patient DIR for two highly deformable organs-the bladder and the rectum-in prostate cancer RT using a quantitative metric based on multiple image registration, the distance discordance metric (DDM). Voxel-by-voxel DIR uncertainties of the bladder and rectum were evaluated using DDM on weekly CT scans of 38 subjects previously treated with RT for prostate cancer (six scans/subject). The DDM was obtained from group-wise B-spline registration of each patient's collection of repeat CT scans. For each structure, registration uncertainties were derived from DDM-related metrics. In addition, five other quantitative measures, including inverse consistency error (ICE), transitivity error (TE), Dice similarity (DSC) and volume ratios between corresponding structures from pre- and post- registered images were computed and compared with the DDM. The DDM varied across subjects and structures; DDMmean of the bladder ranged from 2 to 13 mm and from 1 to 11 mm for the rectum. There was a high correlation between DDMmean of the bladder and the rectum (Pearson's correlation coefficient, R p  =  0.62). The correlation between DDMmean and the volume ratios post-DIR was stronger (R p  =  0.51; 0.68) than the correlation with the TE (bladder: R p  =  0.46; rectum: R p  =  0.47), or the ICE (bladder: R p  =  0.34; rectum: R p  =  0.37). There was a negative correlation between DSC and DDMmean of both the bladder (R p  =  -0.23) and the rectum (R p  =  -0.63). The DDM uncertainty metric indicated considerable DIR variability across subjects and structures. Our

  11. A comparative study between evaluation methods for quality control procedures for determining the accuracy of PET/CT registration

    NASA Astrophysics Data System (ADS)

    Cha, Min Kyoung; Ko, Hyun Soo; Jung, Woo Young; Ryu, Jae Kwang; Choe, Bo-Young

    2015-08-01

    The Accuracy of registration between positron emission tomography (PET) and computed tomography (CT) images is one of the important factors for reliable diagnosis in PET/CT examinations. Although quality control (QC) for checking alignment of PET and CT images should be performed periodically, the procedures have not been fully established. The aim of this study is to determine optimal quality control (QC) procedures that can be performed at the user level to ensure the accuracy of PET/CT registration. Two phantoms were used to carry out this study: the American college of Radiology (ACR)-approved PET phantom and National Electrical Manufacturers Association (NEMA) International Electrotechnical Commission (IEC) body phantom, containing fillable spheres. All PET/CT images were acquired on a Biograph TruePoint 40 PET/CT scanner using routine protocols. To measure registration error, the spatial coordinates of the estimated centers of the target slice (spheres) was calculated independently for the PET and the CT images in two ways. We compared the images from the ACR-approved PET phantom to that from the NEMA IEC body phantom. Also, we measured the total time required from phantom preparation to image analysis. The first analysis method showed a total difference of 0.636 ± 0.11 mm for the largest hot sphere and 0.198 ± 0.09 mm for the largest cold sphere in the case of the ACR-approved PET phantom. In the NEMA IEC body phantom, the total difference was 3.720 ± 0.97 mm for the largest hot sphere and 4.800 ± 0.85 mm for the largest cold sphere. The second analysis method showed that the differences in the x location at the line profile of the lesion on PET and CT were (1.33, 1.33) mm for a bone lesion, (-1.26, -1.33) mm for an air lesion and (-1.67, -1.60) mm for a hot sphere lesion for the ACR-approved PET phantom. For the NEMA IEC body phantom, the differences in the x location at the line profile of the lesion on PET and CT were (-1.33, 4.00) mm for the air

  12. Understanding the nanoparticle–protein corona using methods to quantify exchange rates and affinities of proteins for nanoparticles

    PubMed Central

    Cedervall, Tommy; Lynch, Iseult; Lindman, Stina; Berggård, Tord; Thulin, Eva; Nilsson, Hanna; Dawson, Kenneth A.; Linse, Sara

    2007-01-01

    Due to their small size, nanoparticles have distinct properties compared with the bulk form of the same materials. These properties are rapidly revolutionizing many areas of medicine and technology. Despite the remarkable speed of development of nanoscience, relatively little is known about the interaction of nanoscale objects with living systems. In a biological fluid, proteins associate with nanoparticles, and the amount and presentation of the proteins on the surface of the particles leads to an in vivo response. Proteins compete for the nanoparticle “surface,” leading to a protein “corona” that largely defines the biological identity of the particle. Thus, knowledge of rates, affinities, and stoichiometries of protein association with, and dissociation from, nanoparticles is important for understanding the nature of the particle surface seen by the functional machinery of cells. Here we develop approaches to study these parameters and apply them to plasma and simple model systems, albumin and fibrinogen. A series of copolymer nanoparticles are used with variation of size and composition (hydrophobicity). We show that isothermal titration calorimetry is suitable for studying the affinity and stoichiometry of protein binding to nanoparticles. We determine the rates of protein association and dissociation using surface plasmon resonance technology with nanoparticles that are thiol-linked to gold, and through size exclusion chromatography of protein–nanoparticle mixtures. This method is less perturbing than centrifugation, and is developed into a systematic methodology to isolate nanoparticle-associated proteins. The kinetic and equilibrium binding properties depend on protein identity as well as particle surface characteristics and size. PMID:17267609

  13. Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

    PubMed Central

    Zhao, Huaying; Schuck, Peter

    2015-01-01

    Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design. PMID:25615855

  14. Direct Delta-MBPT(2) method for ionization potentials, electron affinities, and excitation energies using fractional occupation numbers

    SciTech Connect

    Beste, Ariana; Vazquez-Mayagoitia, Alvaro; Ortiz, J. Vincent

    2013-01-01

    A direct method (D-Delta-MBPT(2)) to calculate second-order ionization potentials (IPs), electron affinities (EAs), and excitation energies is developed. The Delta-MBPT(2) method is defined as the correlated extension of the Delta-HF method. Energy differences are obtained by integrating the energy derivative with respect to occupation numbers over the appropriate parameter range. This is made possible by writing the second-order energy as a function of the occupation numbers. Relaxation effects are fully included at the SCF level. This is in contrast to linear response theory, which makes the D-Delta-MBPT(2) applicable not only to single excited but also higher excited states. We show the relationship of the D-Delta-MBPT(2) method for IPs and EAs to a second-order approximation of the effective Fock-space coupled-cluster Hamiltonian and a second-order electron propagator method. We also discuss the connection between the D-Delta-MBPT(2) method for excitation energies and the CIS-MP2 method. Finally, as a proof of principle, we apply our method to calculate ionization potentials and excitation energies of some small molecules. For IPs, the Delta-MBPT(2) results compare well to the second-order solution of the Dyson equation. For excitation energies, the deviation from EOM-CCSD increases when correlation becomes more important. When using the numerical integration technique, we encounter difficulties that prevented us from reaching the Delta-MBPT(2) values. Most importantly, relaxation beyond the Hartree Fock level is significant and needs to be included in future research.

  15. The Intego database: background, methods and basic results of a Flemish general practice-based continuous morbidity registration project

    PubMed Central

    2014-01-01

    Background Intego is the only operational computerized morbidity registration network in Belgium based on general practice data. Intego collects data from over 90 general practitioners. All the information is routinely collected in the electronic health record during daily practice. Methods In this article we describe the design and methods used within the Intego network together with some of its basic results. The collected data, the quality control procedures, the ethical-legal aspects and the statistical procedures are discussed. Results Intego contains longitudinal information on 285 357 different patients, corresponding to over 2.3% of the Flemish population representative in terms of age and sex. More than 3 million diagnoses, 12 million drug prescriptions and 29 million laboratory tests have been recorded. Conclusions Intego enables us to present and compare data on health parameters, incidence and prevalence rates, laboratory results, and prescribed drugs for all relevant subgroups on a routine basis and is unique in Belgium. PMID:24906941

  16. A new method for real-time co-registration of 3D coronary angiography and intravascular ultrasound or optical coherence tomography.

    PubMed

    Carlier, Stéphane; Didday, Rich; Slots, Tristan; Kayaert, Peter; Sonck, Jeroen; El-Mourad, Mike; Preumont, Nicolas; Schoors, Dany; Van Camp, Guy

    2014-06-01

    We present a new clinically practical method for online co-registration of 3D quantitative coronary angiography (QCA) and intravascular ultrasound (IVUS) or optical coherence tomography (OCT). The workflow is based on two modified commercially available software packages. Reconstruction steps are explained and compared to previously available methods. The feasibility for different clinical scenarios is illustrated. The co-registration appears accurate, robust and induced a minimal delay on the normal cath lab activities. This new method is based on the 3D angiographic reconstruction of the catheter path and does not require operator's identification of landmarks to establish the image synchronization. PMID:24746102

  17. Registration of heat capacity mapping mission day and night images

    NASA Technical Reports Server (NTRS)

    Watson, K.; Hummer-Miller, S.; Sawatzky, D. L.

    1982-01-01

    Registration of thermal images is complicated by distinctive differences in the appearance of day and night features needed as control in the registration process. These changes are unlike those that occur between Landsat scenes and pose unique constraints. Experimentation with several potentially promising techniques has led to selection of a fairly simple scheme for registration of data from the experimental thermal satellite HCMM using an affine transformation. Two registration examples are provided.

  18. Global Multi-Method Analysis of Affinities and Cooperativity in Complex Systems of Macromolecular Interactions

    PubMed Central

    Zhao, Huaying; Schuck, Peter

    2012-01-01

    Cooperativity, multi-site and multi-component interactions are hallmarks of biological systems of interacting macromolecules. Their thermodynamic characterization is often very challenging due to the notoriously low information content of binding isotherms. We introduce a strategy for the global multi-method analysis of data from multiple techniques (GMMA) that exploits enhanced information content emerging from the mutual constraints of the simultaneous modeling of orthogonal observables from calorimetric, spectroscopic, hydrodynamic, biosensing, or other thermodynamic binding experiments. We describe new approaches to address statistical problems that arise in the analysis of dissimilar data sets. The GMMA approach can significantly increase the complexity of interacting systems that can be accurately thermodynamically characterized. PMID:23020071

  19. Nonrigid 3D medical image registration and fusion based on deformable models.

    PubMed

    Liu, Peng; Eberhardt, Benjamin; Wybranski, Christian; Ricke, Jens; Lüdemann, Lutz

    2013-01-01

    For coregistration of medical images, rigid methods often fail to provide enough freedom, while reliable elastic methods are available clinically for special applications only. The number of degrees of freedom of elastic models must be reduced for use in the clinical setting to archive a reliable result. We propose a novel geometry-based method of nonrigid 3D medical image registration and fusion. The proposed method uses a 3D surface-based deformable model as guidance. In our twofold approach, the deformable mesh from one of the images is first applied to the boundary of the object to be registered. Thereafter, the non-rigid volume deformation vector field needed for registration and fusion inside of the region of interest (ROI) described by the active surface is inferred from the displacement of the surface mesh points. The method was validated using clinical images of a quasirigid organ (kidney) and of an elastic organ (liver). The reduction in standard deviation of the image intensity difference between reference image and model was used as a measure of performance. Landmarks placed at vessel bifurcations in the liver were used as a gold standard for evaluating registration results for the elastic liver. Our registration method was compared with affine registration using mutual information applied to the quasi-rigid kidney. The new method achieved 15.11% better quality with a high confidence level of 99% for rigid registration. However, when applied to the quasi-elastic liver, the method has an averaged landmark dislocation of 4.32 mm. In contrast, affine registration of extracted livers yields a significantly (P = 0.000001) smaller dislocation of 3.26 mm. In conclusion, our validation shows that the novel approach is applicable in cases where internal deformation is not crucial, but it has limitations in cases where internal displacement must also be taken into account. PMID:23690883

  20. A new real-time method for investigation of affinity properties and binding kinetics of magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Orlov, Alexey V.; Nikitin, Maxim P.; Bragina, Vera A.; Znoyko, Sergey L.; Zaikina, Marina N.; Ksenevich, Tatiana I.; Gorshkov, Boris G.; Nikitin, Petr I.

    2015-04-01

    A method for quantitative investigation of affinity constants of receptors immobilized on magnetic nanoparticles (MP) is developed based on spectral correlation interferometry (SCI). The SCI records with a picometer resolution the thickness changes of a layer of molecules or nanoparticles due to a biochemical reaction on a cover slip, averaged over the sensing area. The method is compatible with other types of sensing surfaces employed in biosensing. The measured values of kinetic association constants of magnetic nanoparticles are 4 orders of magnitude higher than those of molecular antibody association with antigen. The developed method also suggests highly sensitive detection of antigens in a wide dynamic range. The limit of detection of 92 pg/ml has been demonstrated for prostate-specific antigen (PSA) with 50-nm MP employed as labels, which produce 3-order amplification of the SCI signals. The calibration curve features high sensitivity (slope) of 3-fold signal raise per 10-fold increase of PSA concentration within 4-order dynamic range, which is an attractive compromise for precise quantitative and highly sensitive immunoassay. The proposed biosensing technique offers inexpensive disposable sensor chips of cover slips and represents an economically sound alternative to traditional immunoassays for disease diagnostics, detection of pathogens in food and environmental monitoring.

  1. [Affinity chromatography and proteomic screening as the effective method for S100A4 new protein targets discovery].

    PubMed

    Koshelev, Iu A

    2014-01-01

    Affinity chromatography followed by a selective binding proteins identification can be using as effective method for a biological impotent interactions discovery. The molecular structure and their surface charge as and conformational regulation possibilities, which change their surface hydrophobic properties, all they should to taken in account during method optimization process. With the same' method we had identify some new S100A4 target proteins such as cytoskeleton proteins Sept2, Sept7, Sept11 and this interaction would can to highlight as S100A4 would regulate cell motility. Even we had identify the transcription cofactor Ddx5 and through such complex formation a S100A4 protein would can to regulate E-cadherin, p21 Waf1/Cip1), Bnip3 gene expression. The same protocol can be using for a target proteins search with another S100 protein family members, because their molecules demonstrate a high homology level in amino aside sequences and 3D structures. PMID:25842873

  2. A coarse-to-fine automatic and robust registration method for multi-source remote sensing images based on Harris and phase information

    NASA Astrophysics Data System (ADS)

    Li, Haichao; Man, Yiyun

    2015-10-01

    The image phase coherences (PCs) remain invariant when brightness and contrast changes. A new method of remote sensing image registration is proposed. PCs are firstly extracted from the reference image and the input image. In order to improve the registration efficiency, in the first step the PCs are firstly down-sampled using Gaussian pyramid method, and the coarse translation parameters are calculated using phase correlation. In the second step, Harris corners are detected from the two images, and normalized cross-correlation (NCC) function based on PCs is used to find the corresponding matching corners of the two images, and then obtain parameters of an alignment transform model. Experiments have demonstrated that the coarse-to-fine method can be successfully applied to multi-source images registration.

  3. Miniaturized reaction vessel system, method for performing site-specific biochemical reactions and affinity fractionation for use in DNA sequencing

    DOEpatents

    Mirzabekov, Andrei Darievich; Lysov, Yuri Petrovich; Dubley, Svetlana A.

    2000-01-01

    A method for fractionating and sequencing DNA via affinity interaction is provided comprising contacting cleaved DNA to a first array of oligonucleotide molecules to facilitate hybridization between said cleaved DNA and the molecules; extracting the hybridized DNA from the molecules; contacting said extracted hybridized DNA with a second array of oligonucleotide molecules, wherein the oligonucleotide molecules in the second array have specified base sequences that are complementary to said extracted hybridized DNA; and attaching labeled DNA to the second array of oligonucleotide molecules, wherein the labeled re-hybridized DNA have sequences that are complementary to the oligomers. The invention further provides a method for performing multi-step conversions of the chemical structure of compounds comprising supplying an array of polyacrylamide vessels separated by hydrophobic surfaces; immobilizing a plurality of reactants, such as enzymes, in the vessels so that each vessel contains one reactant; contacting the compounds to each of the vessels in a predetermined sequence and for a sufficient time to convert the compounds to a desired state; and isolating the converted compounds from said array.

  4. Preliminary experience with a novel method of three-dimensional co-registration of prostate cancer digital histology and in vivo multiparametric MRI

    PubMed Central

    Orczyk, C.; Rusinek, H.; Rosenkrantz, A.B.; Mikheev, A.; Deng, F.-M.; Melamed, J.; Taneja, S.S.

    2013-01-01

    AIM To assess a novel method of three-dimensional (3D) co-registration of prostate cancer digital histology and in-vivo multiparametric magnetic resonance imaging (mpMRI) image sets for clinical usefulness. MATERIAL AND METHODS A software platform was developed to achieve 3D co- registration. This software was prospectively applied to three patients who underwent radical prostatectomy. Data comprised in-vivo mpMRI [T2-weighted, dynamic contrast-enhanced weighted images (DCE); apparent diffusion coefficient (ADC)], ex-vivo T2-weighted imaging, 3D-rebuilt pathological specimen, and digital histology. Internal landmarks from zonal anatomy served as reference points for assessing co-registration accuracy and precision. RESULTS Applying a method of deformable transformation based on 22 internal landmarks, a 1.6 mm accuracy was reached to align T2-weighted images and the 3D-rebuilt pathological specimen, an improvement over rigid transformation of 32% (p = 0.003). The 22 zonal anatomy landmarks were more accurately mapped using deformable transformation than rigid transformation (p = 0.0008). An automatic method based on mutual information, enabled automation of the process and to include perfusion and diffusion MRI images. Evaluation of co-registration accuracy using the volume overlap index (Dice index) met clinically relevant requirements, ranging from 0.81–0.96 for sequences tested. Ex-vivo images of the specimen did not significantly improve co-registration accuracy. CONCLUSION This preliminary analysis suggests that deformable transformation based on zonal anatomy landmarks is accurate in the co-registration of mpMRI and histology. Including diffusion and perfusion sequences in the same 3D space as histology is essential further clinical information. The ability to localize cancer in 3D space may improve targeting for image-guided biopsy, focal therapy, and disease quantification in surveillance protocols. PMID:23993149

  5. Toward a Universal Method for Preparing Molecularly Imprinted Polymer Nanoparticles with Antibody-like Affinity for Proteins.

    PubMed

    Xu, Jingjing; Ambrosini, Serena; Tamahkar, Emel; Rossi, Claire; Haupt, Karsten; Tse Sum Bui, Bernadette

    2016-01-11

    We describe a potentially universal, simple and cheap method to prepare water-compatible molecularly imprinted polymer nanoparticles (MIP-NPs) as synthetic antibodies against proteins. The strategy is based on a solid phase synthesis approach where glass beads (GBs) are functionalized with a metal chelate, acting as a general affinity ligand to attract surface-bound histidines present on proteins. This configuration enables an oriented immobilization of the proteins, upon which thermoresponsive MIP-NPs are synthesized. The GBs play the role of both a reactor and a separation column since, after synthesis, the MIP-NPs are released from the support by a simple temperature change, resulting in protein-free polymers. The resulting MIP-NPs are endowed with improved binding site homogeneity, since the binding sites have the same orientation. Moreover, they are stable (no aggregation) in a buffer solution for prolonged storage time and exhibit apparent dissociation constants in the nanomolar range, with little or no cross-reactivity toward other proteins. PMID:26644006

  6. A gaussian mixture + demons deformable registration method for cone-beam CT-guided robotic transoral base-of-tongue surgery

    NASA Astrophysics Data System (ADS)

    Reaungamornrat, S.; Liu, W. P.; Schafer, S.; Otake, Y.; Nithiananthan, S.; Uneri, A.; Richmon, J.; Sorger, J.; Siewerdsen, J. H.; Taylor, R. H.

    2013-03-01

    Purpose: An increasingly popular minimally invasive approach to resection of oropharyngeal / base-of-tongue cancer is made possible by a transoral technique conducted with the assistance of a surgical robot. However, the highly deformed surgical setup (neck flexed, mouth open, and tongue retracted) compared to the typical patient orientation in preoperative images poses a challenge to guidance and localization of the tumor target and adjacent critical anatomy. Intraoperative cone-beam CT (CBCT) can account for such deformation, but due to the low contrast of soft-tissue in CBCT images, direct localization of the target and critical tissues in CBCT images can be difficult. Such structures may be more readily delineated in preoperative CT or MR images, so a method to deformably register such information to intraoperative CBCT could offer significant value. This paper details the initial implementation of a deformable registration framework to align preoperative images with the deformed intraoperative scene and gives preliminary evaluation of the geometric accuracy of registration in CBCT-guided TORS. Method: The deformable registration aligns preoperative CT or MR to intraoperative CBCT by integrating two established approaches. The volume of interest is first segmented (specifically, the region of the tongue from the tip to the hyoid), and a Gaussian mixture (GM) mode1 of surface point clouds is used for rigid initialization (GMRigid) as well as an initial deformation (GMNonRigid). Next, refinement of the registration is performed using the Demons algorithm applied to distance transformations of the GM-registered and CBCT volumes. The registration accuracy of the framework was quantified in preliminary studies using a cadaver emulating preoperative and intraoperative setups. Geometric accuracy of registration was quantified in terms of target registration error (TRE) and surface distance error. Result: With each

  7. A registration-based segmentation method with application to adiposity analysis of mice microCT images

    NASA Astrophysics Data System (ADS)

    Bai, Bing; Joshi, Anand; Brandhorst, Sebastian; Longo, Valter D.; Conti, Peter S.; Leahy, Richard M.

    2014-04-01

    Obesity is a global health problem, particularly in the U.S. where one third of adults are obese. A reliable and accurate method of quantifying obesity is necessary. Visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) are two measures of obesity that reflect different associated health risks, but accurate measurements in humans or rodent models are difficult. In this paper we present an automatic, registration-based segmentation method for mouse adiposity studies using microCT images. We co-register the subject CT image and a mouse CT atlas. Our method is based on surface matching of the microCT image and an atlas. Surface-based elastic volume warping is used to match the internal anatomy. We acquired a whole body scan of a C57BL6/J mouse injected with contrast agent using microCT and created a whole body mouse atlas by manually delineate the boundaries of the mouse and major organs. For method verification we scanned a C57BL6/J mouse from the base of the skull to the distal tibia. We registered the obtained mouse CT image to our atlas. Preliminary results show that we can warp the atlas image to match the posture and shape of the subject CT image, which has significant differences from the atlas. We plan to use this software tool in longitudinal obesity studies using mouse models.

  8. Convex hull matching and hierarchical decomposition for multimodality medical image registration.

    PubMed

    Yang, Jian; Fan, Jingfan; Fu, Tianyu; Ai, Danni; Zhu, Jianjun; Li, Qin; Wang, Yongtian

    2015-01-01

    This study proposes a novel hierarchical pyramid strategy for 3D registration of multimodality medical images. The surfaces of the source and target volume data are first extracted, and the surface point clouds are then aligned roughly using convex hull matching. The convex hull matching registration procedure could align images with large-scale transformations. The original images are divided into blocks and the corresponding blocks in the two images are registered by affine and non-rigid registration procedures. The sub-blocks are iteratively smoothed by the Gaussian kernel with different sizes during the registration procedure. The registration result of the large kernel is taken as the input of the small kernel registration. The fine registration of the two volume data sets is achieved by iteratively increasing the number of blocks, in which increase in similarity measure is taken as a criterion for acceptation of each iteration level. Results demonstrate the effectiveness and robustness of the proposed method in registering the multiple modalities of medical images. PMID:25882735

  9. Computed tomography calcium score scan for attenuation correction of N-13 ammonia cardiac positron emission tomography: effect of respiratory phase and registration method.

    PubMed

    Zaidi, Habib; Nkoulou, Rene; Bond, Sarah; Baskin, Aylin; Schindler, Thomas; Ratib, Osman; Declerck, Jerome

    2013-08-01

    The use of coronary calcium scoring (CaScCT) for attenuation correction (AC) of (13)N-ammonia PET/CT studies (NH3) is still being debated. We compare standard ACCT to CaScCT using various respiratory phases and co-registration methods for AC. Forty-one patients underwent a stress/rest NH3. Standard ACCT scans and CaScCT acquired during inspiration (CaScCTinsp, 26 patients) or expiration (CaScCTexp, 15 patients) were used to correct PET data for photon attenuation. Resulting images were compared using Pearson's correlation and Bland-Altman (BA) limits of agreement (LA) on segmental relative and absolute coronary blood flow (CBF) using both manual and automatic co-registration methods (rigid-body and deformable). For relative perfusion, CaScCTexp correlates better than CaScCTinsp with ACCT when using manual co-registration (r = 0.870; P < 0.001 and r = 0.732; P < 0.001, respectively). Automatic co-registration provides the best correlation between CaScCTexp and ACCT for relative perfusion (r = 0.956; P < 0.001). Both CaScCTinsp and CaScCTexp yielded excellent correlations with ACCT for CBF when using manual co-registration (r = 0.918; P < 0.001; BA mean bias 0.05 ml/min/g; LA: -0.42 to +0.3 ml/min/g and r = 0.97; P < 0.001; BA mean bias 0.1 ml/min/g; LA: -0.65 to +0.5 ml/min/g, respectively). The use of CaScCTexp and deformable co-registration is best suited for AC to quantify relative perfusion and CBF enabling substantial radiation dose reduction. PMID:23504215

  10. A local fast marching-based diffusion tensor image registration algorithm by simultaneously considering spatial deformation and tensor orientation.

    PubMed

    Xue, Zhong; Li, Hai; Guo, Lei; Wong, Stephen T C

    2010-08-01

    It is a key step to spatially align diffusion tensor images (DTI) to quantitatively compare neural images obtained from different subjects or the same subject at different timepoints. Different from traditional scalar or multi-channel image registration methods, tensor orientation should be considered in DTI registration. Recently, several DTI registration methods have been proposed in the literature, but deformation fields are purely dependent on the tensor features not the whole tensor information. Other methods, such as the piece-wise affine transformation and the diffeomorphic non-linear registration algorithms, use analytical gradients of the registration objective functions by simultaneously considering the reorientation and deformation of tensors during the registration. However, only relatively local tensor information such as voxel-wise tensor-similarity is utilized. This paper proposes a new DTI image registration algorithm, called local fast marching (FM)-based simultaneous registration. The algorithm not only considers the orientation of tensors during registration but also utilizes the neighborhood tensor information of each voxel to drive the deformation, and such neighborhood tensor information is extracted from a local fast marching algorithm around the voxels of interest. These local fast marching-based tensor features efficiently reflect the diffusion patterns around each voxel within a spherical neighborhood and can capture relatively distinctive features of the anatomical structures. Using simulated and real DTI human brain data the experimental results show that the proposed algorithm is more accurate compared with the FA-based registration and is more efficient than its counterpart, the neighborhood tensor similarity-based registration. PMID:20382233

  11. Application of a constrained regularization method to extraction of affinity distributions: proton and metal binding to humic substances.

    PubMed

    Orsetti, Silvia; Andrade, Estela María; Molina, Fernando V

    2009-08-15

    The binding of proton and metal cations to humic substances has been analyzed with a regularized fitting procedure (using the CONTIN software package) to extract conditional affinity distributions, valid at a given ionic strength, from binding (titration) curves. The procedure was previously tested with simulated titration curves using a simple bi-Gaussian model, the NICA-Donnan model, and the Stockholm humic model. Application to literature data for proton binding shows that in several cases the affinity distribution found is bimodal (carboxylic and phenolic sites) as usually assumed; however in other cases, specially for fulvic acids, a trimodal distribution is clearly discerned, with a smaller peak between the two noted above attributed to the presence of vicinal carboxylic groups. The analysis of metal binding curves has been performed in a few cases where the available data could be reliably processed, separating the proton affinity distribution and obtaining the conditional affinity spectra. For Cd(II) and Pb(II) a bimodal distribution is found, attributed in principle to mono- and bidentate binding, based on spectroscopic data. In the case of Cu(II), a more complex affinity distribution is found showing 3-4 peaks; this is consistent with spectroscopic studies, where different binding modes, up to tetradentate, have been observed. PMID:19477457

  12. Bilirubin removal from human plasma by Cibacron Blue F3GA using immobilized microporous affinity membranous capillary method.

    PubMed

    Zhang, Lei; Jin, Gu

    2005-07-01

    A novel affinity sorbent system for direct bilirubin removal from human plasma was developed. These new adsorbents comprise Cibacron Blue F3GA as the specific ligand, and microporous membranous poly(tetrafluoroethylene) capillary (modified by coating with a hydrophilic layer of poly(vinyl alcohol) after activation) as the carrier matrix. The affinity adsorbents carrying 126.5 micromol Cibacron Blue F3GA/g polymer was then used to remove bilirubin in a flow-injection system. Non-specific adsorption on the poly(vinyl alcohol) coated capillary remains low, and higher affinity adsorption capacity, of up to 76.2 mg/g polymer was obtained after dye immobilization. The bilirubin adsorption capacity of the affinity capillary decreased with increase in the recirculation rate of plasma. The adsorption capacity increased with increase the temperature while decreased with increase the ionic strength. The maximum adsorption was only observed in neutral solution (pH 6-7). The adsorption isotherm fitted the Langmuir model well. These new adsorbents have higher velocity of mass transfer, better adsorption capacity, less fouling, longer service life and good reusability. The results of blood tests suggested the dye affinity capillary has good blood compatibility. PMID:15894520

  13. SU-E-J-114: A Practical Hybrid Method for Improving the Quality of CT-CBCT Deformable Image Registration for Head and Neck Radiotherapy

    SciTech Connect

    Liu, C; Kumarasiri, A; Chetvertkov, M; Gordon, J; Chetty, I; Siddiqui, F; Kim, J

    2015-06-15

    Purpose: Accurate deformable image registration (DIR) between CT and CBCT in H&N is challenging. In this study, we propose a practical hybrid method that uses not only the pixel intensities but also organ physical properties, structure volume of interest (VOI), and interactive local registrations. Methods: Five oropharyngeal cancer patients were selected retrospectively. For each patient, the planning CT was registered to the last fraction CBCT, where the anatomy difference was largest. A three step registration strategy was tested; Step1) DIR using pixel intensity only, Step2) DIR with additional use of structure VOI and rigidity penalty, and Step3) interactive local correction. For Step1, a public-domain open-source DIR algorithm was used (cubic B-spline, mutual information, steepest gradient optimization, and 4-level multi-resolution). For Step2, rigidity penalty was applied on bony anatomies and brain, and a structure VOI was used to handle the body truncation such as the shoulder cut-off on CBCT. Finally, in Step3, the registrations were reviewed on our in-house developed software and the erroneous areas were corrected via a local registration using level-set motion algorithm. Results: After Step1, there were considerable amount of registration errors in soft tissues and unrealistic stretching in the posterior to the neck and near the shoulder due to body truncation. The brain was also found deformed to a measurable extent near the superior border of CBCT. Such errors could be effectively removed by using a structure VOI and rigidity penalty. The rest of the local soft tissue error could be corrected using the interactive software tool. The estimated interactive correction time was approximately 5 minutes. Conclusion: The DIR using only the image pixel intensity was vulnerable to noise and body truncation. A corrective action was inevitable to achieve good quality of registrations. We found the proposed three-step hybrid method efficient and practical for CT

  14. Affinity chromatography: a historical perspective.

    PubMed

    Hage, David S; Matsuda, Ryan

    2015-01-01

    Affinity chromatography is one of the most selective and versatile forms of liquid chromatography for the separation or analysis of chemicals in complex mixtures. This method makes use of a biologically related agent as the stationary phase, which provides an affinity column with the ability to bind selectively and reversibly to a given target in a sample. This review examines the early work in this method and various developments that have lead to the current status of this technique. The general principles of affinity chromatography are briefly described as part of this discussion. Past and recent efforts in the generation of new binding agents, supports, and immobilization methods for this method are considered. Various applications of affinity chromatography are also summarized, as well as the influence this field has played in the creation of other affinity-based separation or analysis methods. PMID:25749941

  15. Fast and robust 3D ultrasound registration--block and game theoretic matching.

    PubMed

    Banerjee, Jyotirmoy; Klink, Camiel; Peters, Edward D; Niessen, Wiro J; Moelker, Adriaan; van Walsum, Theo

    2015-02-01

    Real-time 3D US has potential for image guidance in minimally invasive liver interventions. However, motion caused by patient breathing makes it hard to visualize a localized area, and to maintain alignment with pre-operative information. In this work we develop a fast affine registration framework to compensate in real-time for liver motion/displacement due to breathing. The affine registration of two consecutive ultrasound volumes in time is performed using block-matching. For a set of evenly distributed points in one volume and their correspondences in the other volume, we propose a robust outlier rejection method to reject false matches. The inliers are then used to determine the affine transformation. The approach is evaluated on 13 4D ultrasound sequences acquired from 8 subjects. For 91 pairs of 3D ultrasound volumes selected from these sequences, a mean registration error of 1.8mm is achieved. A graphics processing unit (GPU) implementation runs the 3D US registration at 8 Hz. PMID:25484018

  16. Overview of affinity tags for protein purification.

    PubMed

    Kimple, Michelle E; Sondek, John

    2004-09-01

    Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, and for detecting protein-protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future. PMID:18429272

  17. Overview of affinity tags for protein purification.

    PubMed

    Kimple, Michelle E; Brill, Allison L; Pasker, Renee L

    2013-01-01

    Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, as well as for detecting protein-protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future. PMID:24510596

  18. Accuracy assessment of a marker-free method for registration of CT and stereo images applied in image-guided implantology: a phantom study.

    PubMed

    Mohagheghi, Saeed; Ahmadian, Alireza; Yaghoobee, Siamak

    2014-12-01

    To assess the accuracy of a proposed marker-free registration method as opposed to the conventional marker-based method using an image-guided dental system, and investigating the best configurations of anatomical landmarks for various surgical fields in a phantom study, a CT-compatible dental phantom consisting of implanted targets was used. Two marker-free registration methods were evaluated, first using dental anatomical landmarks and second, using a reference marker tool. Six implanted markers, distributed in the inner space of the phantom were used as the targets; the values of target registration error (TRE) for each target were measured and compared with the marker-based method. Then, the effects of different landmark configurations on TRE values, measured using the Parsiss IV Guided Navigation system (Parsiss, Tehran, Iran), were investigated to find the best landmark arrangement for reaching the minimum registration error in each target region. It was proved that marker-free registration can be as precise as the marker-based method. This has a great impact on image-guided implantology systems whereby the drawbacks of fiducial markers for patient and surgeon are removed. It was also shown that smaller values of TRE could be achieved by using appropriate landmark configurations and moving the center of the landmark set closer to the surgery target. Other common factors would not necessarily decrease the TRE value so the conventional rules accepted in the clinical community about the ways to reduce TRE should be adapted to the selected field of dental surgery. PMID:25441868

  19. Enhanced cell affinity of chitosan membranes mediated by superficial cross-linking: a straightforward method attainable by standard laboratory procedures.

    PubMed

    Rodríguez-Velázquez, Eustolia; Silva, Maite; Taboada, Pablo; Mano, João F; Suárez-Quintanilla, David; Alatorre-Meda, Manuel

    2014-01-13

    It is well accepted that the surface modification of biomaterials can improve their biocompatibility. In this context, techniques like ion etching, plasma-mediated chemical functionalization, electrospinning, and contact microprinting have successfully been employed to promote the cell adhesion and proliferation of chitosan (CH) substrates. However, they prove to be time-consuming, highly dependent on environmental conditions, and/or limited to the use of expensive materials and sophisticated instruments not accessible to standard laboratories, hindering to a high extent their straightforward application. Filling this gap, this paper proposes the superficial cross-linking of CH as a much simpler and accessible means to modify its superficial properties in order to enhance its cellular affinity. CH membranes were prepared by solvent casting followed by a cross-linking step mediated by the chemical vapor deposition (CVD) of glutaraldehyde (GA). The membranes were characterized against non- and solution cross-linked membranes in terms of their mechanical/surface properties and biological performance. Among others, the CVD membranes proved (i) to be more mechanically stable against cell culture and sterilization than membranes cross-linked in solution and (ii) to prompt the adherence and sustained proliferation of healthy cells to levels even superior to commercial tissue culture plates (TCPs). Accordingly, the CVD cross-linking approach was demonstrated to be a simple and cost-effective alternative to the aforementioned conventional methods. Interestingly, this concept can also be applied to other biomaterials as long as GA (or other volatile components alike) can be employed as a cross-linker, making possible the cross-linking reaction at mild experimental conditions, neither requiring sophisticated lab implements nor using any potentially harmful procedure. PMID:24328099

  20. A mix-and-read drop-based in vitro two-hybrid method for screening high-affinity peptide binders

    PubMed Central

    Cui, Naiwen; Zhang, Huidan; Schneider, Nils; Tao, Ye; Asahara, Haruichi; Sun, Zhiyi; Cai, Yamei; Koehler, Stephan A.; de Greef, Tom F. A.; Abbaspourrad, Alireza; Weitz, David A.; Chong, Shaorong

    2016-01-01

    Drop-based microfluidics have recently become a novel tool by providing a stable linkage between phenotype and genotype for high throughput screening. However, use of drop-based microfluidics for screening high-affinity peptide binders has not been demonstrated due to the lack of a sensitive functional assay that can detect single DNA molecules in drops. To address this sensitivity issue, we introduced in vitro two-hybrid system (IVT2H) into microfluidic drops and developed a streamlined mix-and-read drop-IVT2H method to screen a random DNA library. Drop-IVT2H was based on the correlation between the binding affinity of two interacting protein domains and transcriptional activation of a fluorescent reporter. A DNA library encoding potential peptide binders was encapsulated with IVT2H such that single DNA molecules were distributed in individual drops. We validated drop-IVT2H by screening a three-random-residue library derived from a high-affinity MDM2 inhibitor PMI. The current drop-IVT2H platform is ideally suited for affinity screening of small-to-medium-sized libraries (103–106). It can obtain hits within a single day while consuming minimal amounts of reagents. Drop-IVT2H simplifies and accelerates the drop-based microfluidics workflow for screening random DNA libraries, and represents a novel alternative method for protein engineering and in vitro directed protein evolution. PMID:26940078

  1. A mix-and-read drop-based in vitro two-hybrid method for screening high-affinity peptide binders.

    PubMed

    Cui, Naiwen; Zhang, Huidan; Schneider, Nils; Tao, Ye; Asahara, Haruichi; Sun, Zhiyi; Cai, Yamei; Koehler, Stephan A; de Greef, Tom F A; Abbaspourrad, Alireza; Weitz, David A; Chong, Shaorong

    2016-01-01

    Drop-based microfluidics have recently become a novel tool by providing a stable linkage between phenotype and genotype for high throughput screening. However, use of drop-based microfluidics for screening high-affinity peptide binders has not been demonstrated due to the lack of a sensitive functional assay that can detect single DNA molecules in drops. To address this sensitivity issue, we introduced in vitro two-hybrid system (IVT2H) into microfluidic drops and developed a streamlined mix-and-read drop-IVT2H method to screen a random DNA library. Drop-IVT2H was based on the correlation between the binding affinity of two interacting protein domains and transcriptional activation of a fluorescent reporter. A DNA library encoding potential peptide binders was encapsulated with IVT2H such that single DNA molecules were distributed in individual drops. We validated drop-IVT2H by screening a three-random-residue library derived from a high-affinity MDM2 inhibitor PMI. The current drop-IVT2H platform is ideally suited for affinity screening of small-to-medium-sized libraries (10(3)-10(6)). It can obtain hits within a single day while consuming minimal amounts of reagents. Drop-IVT2H simplifies and accelerates the drop-based microfluidics workflow for screening random DNA libraries, and represents a novel alternative method for protein engineering and in vitro directed protein evolution. PMID:26940078

  2. Simple Method for Shiga Toxin 2e Purification by Affinity Chromatography via Binding to the Divinyl Sulfone Group

    PubMed Central

    Arimitsu, Hideyuki; Sasaki, Keiko; Kojima, Hiroe; Yanaka, Tadashi; Tsuji, Takao

    2013-01-01

    Here we describe a simple affinity purification method for Shiga toxin 2e (Stx2e), a major causative factor of edema disease in swine. Escherichia coli strain MV1184 transformed with the expression plasmid pBSK-Stx2e produced Stx2e when cultivated in CAYE broth containing lincomycin. Stx2e bound to commercial D-galactose gel, containing α-D-galactose immobilized on agarose resin via a divinyl sulfone linker, and was eluted with phosphate-buffered saline containing 4.5 M MgCl2. A small amount of Stx2e bound to another commercial α-galactose-immobilized agarose resin, but not to β-galactose-immobilized resin. In addition, Stx2e bound to thiophilic adsorbent resin containing β-mercaptoethanol immobilized on agarose resin via a divinyl sulfone, and was purified in the same manner as from D-galactose gel, but the Stx2e sample contained some contamination. These results indicate that Stx2e bound to D-galactose gel mainly through the divinyl sulfone group on the resin and to a lesser extent through α-D-galactose. With these methods, the yields of Stx2e and attenuated mutant Stx2e (mStx2e) from 1 L of culture were approximately 36 mg and 27.7 mg, respectively, and the binding capacity of the D-galactose gel and thiophilic adsorbent resin for Stx2e was at least 20 mg per 1 ml of resin. In addition, using chimeric toxins with prototype Stx2 which did not bind to thiophilic adsorbent resin and some types of mutant Stx2e and Stx2 which contained inserted mutations in the B subunits, we found that, at the least, asparagine (amino acid 17 of the B subunits) was associated with Stx2e binding to the divinyl sulfone group. The mStx2e that was isolated exhibited vaccine effects in ICR mice, indicating that these methods are beneficial for large-scale preparation of Stx2e toxoid, which protects swine from edema disease. PMID:24340102

  3. A novel coarse-to-fine method for registration of multispectral images

    NASA Astrophysics Data System (ADS)

    Jin, Hongbin; Fan, Chunxiao; Li, Yong; Xu, Liangpeng

    2016-07-01

    Due to non-linear intensity changes between multispectral images, the existed descriptors often yield low matching performance. In order to build reliable keypoint mappings on multispectral images, a novel coarse-to-fine method is designed using projective transformation and the information of edge overlap. The method consists of a coarse process and a fine-tuning process. In the coarse process, initial keypoint mappings are built with the descriptors associated with keypoints and the relative distance constraints are employed on them to remove outliers. In the fine-tuning process, the edge overlap information is utilized as similarity metric and an iterative framework is applied to search correct keypoint mappings. The performance of the proposed is investigated with keypoints extracted by speeded-up robust features. The experiment results show that the proposed method can build more reliable keypoint mappings on multispectral images than existed methods.

  4. Performance comparison of rigid and affine models for motion estimation using ultrasound radio-frequency signals.

    PubMed

    Pan, Xiaochang; Liu, Ke; Shao, Jinghua; Gao, Jing; Huang, Lingyun; Bai, Jing; Luo, Jianwen

    2015-11-01

    Tissue motion estimation is widely used in many ultrasound techniques. Rigid-model-based and nonrigid-modelbased methods are two main groups of space-domain methods of tissue motion estimation. The affine model is one of the commonly used nonrigid models. The performances of the rigid model and affine model have not been compared on ultrasound RF signals, which have been demonstrated to obtain higher accuracy, precision, and resolution in motion estimation compared with B-mode images. In this study, three methods, i.e., the normalized cross-correlation method with rigid model (NCC), the optical flow method with rigid model (OFRM), and the optical flow method with affine model (OFAM), are compared using ultrasound RF signals, rather than the B-mode images used in previous studies. Simulations, phantom, and in vivo experiments are conducted to make the comparison. In the simulations, the root-mean-square errors (RMSEs) of axial and lateral displacements and strains are used to assess the accuracy of motion estimation, and the elastographic signal-tonoise ratio (SNRe) and contrast-to-noise ratio (CNRe) are used to evaluate the quality of axial strain images. In the phantom experiments, the registration error between the pre- and postdeformation RF signals, as well as the SNRe and CNRe of axial strain images, are utilized as the evaluation criteria. In the in vivo experiments, the registration error is used to evaluate the estimation performance. The results show that the affinemodel- based method (i.e., OFAM) obtains the lowest RMSE or registration error and the highest SNRe and CNRe among all the methods. The affine model is demonstrated to be superior to the rigid model in motion estimation based on RF signals. PMID:26559623

  5. Comparative Study of Three Methods for Affinity Measurements: Capillary Electrophoresis Coupled with UV Detection and Mass Spectrometry, and Direct Infusion Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Mironov, Gleb G.; Logie, Jennifer; Okhonin, Victor; Renaud, Justin B.; Mayer, Paul M.; Berezovski, Maxim V.

    2012-07-01

    We present affinity capillary electrophoresis and mass spectrometry (ACE-MS) as a comprehensive separation technique for label-free solution-based affinity analysis. The application of ACE-MS for measuring affinity constants between eight small molecule drugs [ibuprofen, s-flurbiprofen, diclofenac, phenylbutazone, naproxen, folic acid, resveratrol, and 4,4'-(propane-1,3-diyl) dibenzoic acid] and β-cyclodextrin is described. We couple on-line ACE with MS to combine the separation and kinetic capability of ACE together with the molecular weight and structural elucidation of MS in one system. To understand the full potential of ACE-MS, we compare it with two other methods: Direct infusion mass spectrometry (DIMS) and ACE with UV detection (ACE-UV). After the evaluation, DIMS provides less reliable equilibrium dissociation constants than separation-based ACE-UV and ACE-MS, and cannot be used solely for the study of noncovalent interactions. ACE-MS determines apparent dissociation constants for all reacting small molecules in a mixture, even in cases when drugs overlap with each other during separation. The ability of ACE-MS to interact, separate, and rapidly scan through m/z can facilitate the simultaneous affinity analysis of multiple interacting pairs, potentially leading to the high-throughput screening of drug candidates.

  6. SU-C-17A-03: Evaluation of Deformable Image Registration Methods Between MRI and CT for Prostate Cancer Radiotherapy

    SciTech Connect

    Wen, N; Glide-Hurst, C; Zhong, H; Chin, K; Kumarasiri, A; Liu, C; Liu, M; Siddiqui, S

    2014-06-15

    Purpose: We evaluated the performance of two commercially available and one open source B-Spline deformable image registration (DIR) algorithms between T2-weighted MRI and treatment planning CT using the DICE indices. Methods: CT simulation (CT-SIM) and MR simulation (MR-SIM) for four prostate cancer patients were conducted on the same day using the same setup and immobilization devices. CT images (120 kVp, 500 mAs, voxel size = 1.1x1.1x3.0 mm3) were acquired using an open-bore CT scanner. T2-weighted Turbo Spine Echo (T2W-TSE) images (TE/TR/α = 80/4560 ms/90°, voxel size = 0.7×0.7×2.5 mm3) were scanned on a 1.0T high field open MR-SIM. Prostates, seminal vesicles, rectum and bladders were delineated on both T2W-TSE and CT images by the attending physician. T2W-TSE images were registered to CT images using three DIR algorithms, SmartAdapt (Varian), Velocity AI (Velocity) and Elastix (Klein et al 2010) and contours were propagated. DIR results were evaluated quantitatively or qualitatively by image comparison and calculating organ DICE indices. Results: Significant differences in the contours of prostate and seminal vesicles were observed between MR and CT. On average, volume changes of the propagated contours were 5%, 2%, 160% and 8% for the prostate, seminal vesicles, bladder and rectum respectively. Corresponding mean DICE indices were 0.7, 0.5, 0.8, and 0.7. The intraclass correlation coefficient (ICC) was 0.9 among three algorithms for the Dice indices. Conclusion: Three DIR algorithms for CT/MR registration yielded similar results for organ propagation. Due to the different soft tissue contrasts between MRI and CT, organ delineation of prostate and SVs varied significantly, thus efforts to develop other DIR evaluation metrics are warranted. Conflict of interest: Submitting institution has research agreements with Varian Medical System and Philips Healthcare.

  7. Additive method for the prediction of protein-peptide binding affinity. Application to the MHC class I molecule HLA-A*0201.

    PubMed

    Doytchinova, Irini A; Blythe, Martin J; Flower, Darren R

    2002-01-01

    A method has been developed for prediction of binding affinities between proteins and peptides. We exemplify the method through its application to binding predictions of peptides with affinity to major histocompatibility complex class I molecule HLA-A*0201. The method is named "additive" because it is based on the assumption that the binding affinity of a peptide could be presented as a sum of the contributions of the amino acids at each position and the interactions between them. The amino acid contributions and the contributions of the interactions between adjacent side chains and every second side chain were derived using a partial least squares (PLS) statistical methodology using a training set of 420 experimental IC50 values. The predictive power of the method was assessed using rigorous cross-validation and using an independent test set of 89 peptides. The mean value of the residuals between the experimental and predicted pIC50 values was 0.508 for this test set. The additive method was implemented in a program for rapid T-cell epitope search. It is universal and can be applied to any peptide-protein interaction where binding data is known. PMID:12645903

  8. Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods.

    PubMed

    Mikulskis, Paulius; Genheden, Samuel; Rydberg, Patrik; Sandberg, Lars; Olsen, Lars; Ryde, Ulf

    2012-05-01

    We have estimated affinities for the binding of 34 ligands to trypsin and nine guest molecules to three different hosts in the SAMPL3 blind challenge, using the MM/PBSA, MM/GBSA, LIE, continuum LIE, and Glide score methods. For the trypsin challenge, none of the methods were able to accurately predict the experimental results. For the MM/GB(PB)SA and LIE methods, the rankings were essentially random and the mean absolute deviations were much worse than a null hypothesis giving the same affinity to all ligand. Glide scoring gave a Kendall's τ index better than random, but the ranking is still only mediocre, τ = 0.2. However, the range of affinities is small and most of the pairs of ligands have an experimental affinity difference that is not statistically significant. Removing those pairs improves the ranking metric to 0.4-1.0 for all methods except CLIE. Half of the trypsin ligands were non-binders according to the binding assay. The LIE methods could not separate the inactive ligands from the active ones better than a random guess, whereas MM/GBSA and MM/PBSA were slightly better than random (area under the receiver-operating-characteristic curve, AUC = 0.65-0.68), and Glide scoring was even better (AUC = 0.79). For the first host, MM/GBSA and MM/PBSA reproduce the experimental ranking fairly good, with τ = 0.6 and 0.5, respectively, whereas the Glide scoring was considerably worse, with a τ = 0.4, highlighting that the success of the methods is system-dependent. PMID:22198518

  9. Robust registration of longitudinal spine CT.

    PubMed

    Glocker, Ben; Zikic, Darko; Haynor, David R

    2014-01-01

    Accurate and reliable registration of longitudinal spine images is essential for assessment of disease progression and surgical outcome. Implementing a fully automatic and robust registration for clinical use, however, is challenging since standard registration techniques often fail due to poor initial alignment. The main causes of registration failure are the small overlap between scans which focus on different parts of the spine and/or substantial change in shape (e.g. after correction of abnormal curvature) and appearance (e.g. due to surgical implants). To overcome these issues we propose a registration approach which incorporates estimates of vertebrae locations obtained from a learning-based classification method. These location priors are used to initialize the registration and to provide semantic information within the optimization process. Quantitative evaluation on a database of 93 patients with a total of 276 registrations on longitudinal spine CT demonstrate that our registration method significantly reduces the number of failure cases. PMID:25333125

  10. Automatic registration between 3D intra-operative ultrasound and pre-operative CT images of the liver based on robust edge matching

    NASA Astrophysics Data System (ADS)

    Nam, Woo Hyun; Kang, Dong-Goo; Lee, Duhgoon; Lee, Jae Young; Ra, Jong Beom

    2012-01-01

    The registration of a three-dimensional (3D) ultrasound (US) image with a computed tomography (CT) or magnetic resonance image is beneficial in various clinical applications such as diagnosis and image-guided intervention of the liver. However, conventional methods usually require a time-consuming and inconvenient manual process for pre-alignment, and the success of this process strongly depends on the proper selection of initial transformation parameters. In this paper, we present an automatic feature-based affine registration procedure of 3D intra-operative US and pre-operative CT images of the liver. In the registration procedure, we first segment vessel lumens and the liver surface from a 3D B-mode US image. We then automatically estimate an initial registration transformation by using the proposed edge matching algorithm. The algorithm finds the most likely correspondences between the vessel centerlines of both images in a non-iterative manner based on a modified Viterbi algorithm. Finally, the registration is iteratively refined on the basis of the global affine transformation by jointly using the vessel and liver surface information. The proposed registration algorithm is validated on synthesized datasets and 20 clinical datasets, through both qualitative and quantitative evaluations. Experimental results show that automatic registration can be successfully achieved between 3D B-mode US and CT images even with a large initial misalignment.

  11. Method for nanoscale spatial registration of scanning probes with substrates and surfaces

    NASA Technical Reports Server (NTRS)

    Wade, Lawrence A. (Inventor)

    2010-01-01

    Embodiments in accordance with the present invention relate to methods and apparatuses for aligning a scanning probe used to pattern a substrate, by comparing the position of the probe to a reference location or spot on the substrate. A first light beam is focused on a surface of the substrate as a spatial reference point. A second light beam then illuminates the scanning probe being used for patterning. An optical microscope images both the focused light beam, and a diffraction pattern, shadow, or light backscattered by the illuminated scanning probe tip of a scanning probe microscope (SPM), which is typically the tip of the scanning probe on an atomic force microscope (AFM). Alignment of the scanning probe tip relative to the mark is then determined by visual observation of the microscope image. This alignment process may be repeated to allow for modification or changing of the scanning probe microscope tip.

  12. A Method For Simultaneous Registration Of Motion And Electromyography During Walking

    NASA Astrophysics Data System (ADS)

    Giith, V.; Abbink, F.; Heinrichs, W.; Theysohn, H.

    1980-07-01

    The points the movements of which are to be registered are marked by little light sensitive photoamplifiers. These are periodically (50 times per second) exposed to a VÖshaped bright figure projected by a rotating mirror. The pattern of the resulting electrical impulses is analysed by a computer controlled fast digital time counting apparatus with a clock of 100 ns. Is this way we get every 20 ms the respective position of the marked points (up to nine). The results of this method are simular to the well known photographic chronocyclography with the advantage, however, that the momentary positions of the points are calculated on line (accuracy ± 2 mm). In the intervals between the sweeps of the light-figure the computer picks up 8 lines of analogue data, actually the electromyogram of eight different muscles, and stores them, together with the optical data on digital magnetic tape for further evaluation. After the investigation the obtained data are analysed in the following way : 1) Plotting several parameters of positions (angles, c.g.) together with the electromyogram ver-sus time during one step of walking. 2) Calculating the correlation between the patterns of electrical activity of different muscles. 3) Comparison of the results of 1) and 2) between healthy persons and handicapped persons (C.P.), scoliosis, desease of spine, hip and pelvis, etc...).

  13. The investigation of moving dunes over Mars using very high resolution topography and sub pixel co-registration method.

    NASA Astrophysics Data System (ADS)

    Kim, J.; Baik, H.; Seol, H.

    2015-12-01

    Although the origins and processes of Martian aeolian features, especially dunes, have not been fully identified yet, it has been better understood by the orbital observation method which has led to the identification of Martian dune migration such as a case in Nili Patera (Bridges, 2012), and the numerical model employing advanced computational fluid dynamics. Specifically, the recent introduction of very high-resolution image products, such as 25 cm-resolution HiRISE imagery and its precise photogrammetric processor, allows us to trace the estimated, although tiny, dune migration over the Martian surface. In this study, we attempted to improve the accuracy of active dune migration measurements by 1) the introduction of very high resolution ortho images and stereo analysis based on the hierarchical geodetic control (Kim and Muller, 2009) for better initial point settings; and 2) the improved sub-pixel co-registration algorithms using optical flow with a refinement stage based on a least squares correlation conducted on a pyramidal processor. Consequently, this scheme not only measured Martian dune migration more precisely, but it also achieved the extension of 3D observations combining stereo analysis and photoclinometry. The established algorithms have been tested using the HiRISE time series images over several dune fields, such as the Kaiser, Procter, and Rabe craters, which were reported by the Mars Global Digital Dune Database (Hayward et al., 2013). The detected dune migrations were significantly larger than previously reported values. The outcomes in our study will be demonstrated with the quantified values in 2D and volumetric direction. In the future, the method will be further applied to the dune fields in the Mars Global dune database comprehensively and can be compared with the improved General Circulation Model and the numerical simulation.

  14. Nonlinear spatial warping for between-subjects pedobarographic image registration.

    PubMed

    Pataky, T C; Keijsers, N L W; Goulermas, J Y; Crompton, R H

    2009-04-01

    Foot size and shape vary between individuals and the foot adopts arbitrary stance phase postures, so traditional pedobarographic analyses regionalize foot pressure images to afford homologous data comparison. An alternative approach that does not require explicit anatomical labelling and that is used widely in other functional imaging domains is to register images such that homologous structures optimally overlap and then to compare images directly at the pixel level. Image registration represents the preprocessing cornerstone of such pixel-level techniques, so its performance warrants independent attention. The purpose of this study was to evaluate the performance of four between-subjects warping registration algorithms including: Principal Axes (PA), four-parameter Optimal Scaling (OS4), eight-parameter Optimal Projective (OP8), and locally affine Nonlinear (NL). Fifteen subjects performed 10 trials of self-paced walking, and their peak pressure images were registered within-subjects using an optimal rigid body transformation. The resulting mean images were then registered between-subjects using all four methods in all 210 (15x14) subject combinations. All registration methods improved alignment, and each method performed qualitatively well for certain image pairs. However, only the NL consistently performed satisfactorily because of disproportionate anatomical variation in toe lengths and rearfoot/forefoot width, for example. Using three independent image (dis)similarity metrics, MANOVA confirmed that the NL method yielded superior registration performance (p<0.001). These data demonstrate that nonlinear spatial warping is necessary for robust between-subject pedobarographic image registration and, by extension, robust homologous data comparison at the pixel level. PMID:19112023

  15. [The new technologies for the intraoperative registration of the electrically evoked compound action potentials of the acoustical nerve by means of the neural response telemetry method].

    PubMed

    Bakhshinian, V V; Fedoseev, V I; Tavartkiladze, G A

    2015-01-01

    The present article reports the results of a clinical study of the new wireless device CR120 designed for the intraoperative registration of electrode resistance and the electrically evoked compound action potential (EAP) of the acoustical nerve by means of neural response telemetry. The study has demonstrated the high effectiveness of the application of the new wireless device in clinical practice. It was shown that the registration of electrically evoked compound action potential with the help of the CR120 Intraoperative Remote Assistant took 22% less time than by the conventional method (p<0.001). Moreover, the trial revealed the strong correlation between the threshold EAP values recorded with the use of the new device and by the classical method. PMID:26288202

  16. Registration of video sequences from multiple sensors

    NASA Technical Reports Server (NTRS)

    Sharma, Ravi K.; Pavel, Misha

    1997-01-01

    In this paper, we describe an approach for registration of video sequences from a suite of multiple sensors including television, infrared and radar. Video sequences generated by these sensors may contain abrupt changes in local contrast and inconsistent image features, which pose additional difficulties for registration. Our approach to registration addresses the difficulties caused by using multiple sensors. We use a representation for registration that is invariant to local contrast changes, followed by smoothing of the resulting error measure used for registration, for robust estimation of registration parameters. We use an iterative procedure to reduce the effect of inconsistent features. Finally, we describe a method that uses same-sensor registration to aide in performing registration of sequences of video frames across multiple sensors.

  17. A Simple Flow-Cytometric Method Measuring B Cell Surface Immunoglobulin Avidity Enables Characterization of Affinity Maturation to Influenza A Virus

    PubMed Central

    Frank, Gregory M.; Angeletti, Davide; Ince, William L.; Gibbs, James S.; Khurana, Surender; Wheatley, Adam K.; Max, Edward E.; McDermott, Adrian B.; Golding, Hana; Stevens, James; Bennink, Jack R.

    2015-01-01

    ABSTRACT Antibody (Ab) affinity maturation enables an individual to maintain immunity to an increasing number of pathogens within the limits of a total Ig production threshold. A better understanding of this process is critical for designing vaccines that generate optimal Ab responses to pathogens. Our study describes a simple flow-cytometric method that enumerates virus-specific germinal center (GC) B cells as well as their AC50, a measure of Ab avidity, defined as the antigen concentration required to detect 50% of specific B cells. Using a model of mouse Ab responses to the influenza A virus hemagglutinin (IAV HA), we obtained data indicating that AC50 decreases with time postinfection in an affinity maturation-dependent process. As proof of principle of the utility of the method, our data clearly show that relative to intranasal IAV infection, intramuscular immunization against inactivated IAV in adjuvant results in a diminished GC HA B cell response, with increased AC50 correlating with an increased serum Ab off-rate. Enabling simultaneous interrogation of both GC HA B cell quantity and quality, this technique should facilitate study of affinity maturation and rational vaccine design. PMID:26242629

  18. Comparisons of surface vs. volumetric model-based registration methods using single-plane vs. bi-plane fluoroscopy in measuring spinal kinematics.

    PubMed

    Lin, Cheng-Chung; Lu, Tung-Wu; Wang, Ting-Ming; Hsu, Chao-Yu; Shih, Ting-Fang

    2014-02-01

    Several 2D-to-3D image registration methods are available for measuring 3D vertebral motion but their performance has not been evaluated under the same experimental protocol. In this study, four major types of fluoroscopy-to-CT registration methods, with different use of surface vs. volumetric models, and single-plane vs. bi-plane fluoroscopy, were evaluated: STS (surface, single-plane), VTS (volumetric, single-plane), STB (surface, bi-plane) and VTB (volumetric, bi-plane). Two similarity measures were used: 'Contour Difference' for STS and STB and 'Weighted Edge-Matching Score' for VTS and VTB. Two cadaveric porcine cervical spines positioned in a box filled with paraffin and embedded with four radiopaque markers were CT scanned to obtain vertebral models and marker coordinates, and imaged at ten static positions using bi-plane fluoroscopy for subsequent registrations using different methods. The registered vertebral poses were compared to the gold standard poses defined by the marker positions determined using CT and Roentgen stereophotogrammetry analysis. The VTB was found to have the highest precision (translation: 0.4mm; rotation: 0.3°), comparable with the VTS in rotations (0.3°), and the STB in translations (0.6mm). The STS had the lowest precision (translation: 4.1mm; rotation: 2.1°). PMID:24011956

  19. A hybrid method for reliable registration of digitally reconstructed radiographs and kV x-ray images for image-guided radiation therapy for prostate cancer

    NASA Astrophysics Data System (ADS)

    Song, Yulin; Mueller, Boris; Chan, Maria F.; Sim, Sang E.; Mychalczak, Borys; Huang, Xiaolei

    2008-03-01

    Prostate cancer is the most common tumor site treated with intensity modulated radiation therapy (IMRT). However, due to patient and organ motions, treatment-induced physiological changes, and different daily filling in the bladder and rectum, the position of the prostate in relation to the fixed pelvic bone can change significantly. Without a reliable guiding technique, this could result in underdosing the target and overdosing the critical organs. Therefore, image-guided localization of the prostate must be performed prior to each treatment, which led to the development of a new radiation treatment modality, the image-guided radiation therapy (IGRT). One form of IGRT is to implant three gold seed markers into the prostate gland to serve as a fixed reference system. Daily patient setup verification is performed by using the gold seed markers-based image registration rather than the commonly used bony landmarks-based approach. In this paper, we present an efficient and automated method for registering digitally reconstructed radiographs (DRR) and kV X-ray images of the prostate with high accuracy using a hybrid method. Our technique relies on both internal fiducial markers (i.e. gold seed markers) implanted into the prostate and a robust, hybrid 2D registration method using a salient-region based image registration technique. The registration procedure consists of several novel steps. Validation experiments were performed to register DRR and kV X-ray images in anterior-posterior (AP) or lateral views and the results were reviewed by experienced radiation oncology physicists.

  20. MO-C-17A-11: A Segmentation and Point Matching Enhanced Deformable Image Registration Method for Dose Accumulation Between HDR CT Images

    SciTech Connect

    Zhen, X; Chen, H; Zhou, L; Yan, H; Jiang, S; Jia, X; Gu, X; Mell, L; Yashar, C; Cervino, L

    2014-06-15

    Purpose: To propose and validate a novel and accurate deformable image registration (DIR) scheme to facilitate dose accumulation among treatment fractions of high-dose-rate (HDR) gynecological brachytherapy. Method: We have developed a method to adapt DIR algorithms to gynecologic anatomies with HDR applicators by incorporating a segmentation step and a point-matching step into an existing DIR framework. In the segmentation step, random walks algorithm is used to accurately segment and remove the applicator region (AR) in the HDR CT image. A semi-automatic seed point generation approach is developed to obtain the incremented foreground and background point sets to feed the random walks algorithm. In the subsequent point-matching step, a feature-based thin-plate spline-robust point matching (TPS-RPM) algorithm is employed for AR surface point matching. With the resulting mapping, a DVF characteristic of the deformation between the two AR surfaces is generated by B-spline approximation, which serves as the initial DVF for the following Demons DIR between the two AR-free HDR CT images. Finally, the calculated DVF via Demons combined with the initial one serve as the final DVF to map doses between HDR fractions. Results: The segmentation and registration accuracy are quantitatively assessed by nine clinical HDR cases from three gynecological cancer patients. The quantitative results as well as the visual inspection of the DIR indicate that our proposed method can suppress the interference of the applicator with the DIR algorithm, and accurately register HDR CT images as well as deform and add interfractional HDR doses. Conclusions: We have developed a novel and robust DIR scheme that can perform registration between HDR gynecological CT images and yield accurate registration results. This new DIR scheme has potential for accurate interfractional HDR dose accumulation. This work is supported in part by the National Natural ScienceFoundation of China (no 30970866 and no

  1. Prostate CT segmentation method based on nonrigid registration in ultrasound-guided CT-based HDR prostate brachytherapy

    SciTech Connect

    Yang, Xiaofeng Rossi, Peter; Ogunleye, Tomi; Marcus, David M.; Jani, Ashesh B.; Curran, Walter J.; Liu, Tian; Mao, Hui

    2014-11-01

    Purpose: The technological advances in real-time ultrasound image guidance for high-dose-rate (HDR) prostate brachytherapy have placed this treatment modality at the forefront of innovation in cancer radiotherapy. Prostate HDR treatment often involves placing the HDR catheters (needles) into the prostate gland under the transrectal ultrasound (TRUS) guidance, then generating a radiation treatment plan based on CT prostate images, and subsequently delivering high dose of radiation through these catheters. The main challenge for this HDR procedure is to accurately segment the prostate volume in the CT images for the radiation treatment planning. In this study, the authors propose a novel approach that integrates the prostate volume from 3D TRUS images into the treatment planning CT images to provide an accurate prostate delineation for prostate HDR treatment. Methods: The authors’ approach requires acquisition of 3D TRUS prostate images in the operating room right after the HDR catheters are inserted, which takes 1–3 min. These TRUS images are used to create prostate contours. The HDR catheters are reconstructed from the intraoperative TRUS and postoperative CT images, and subsequently used as landmarks for the TRUS–CT image fusion. After TRUS–CT fusion, the TRUS-based prostate volume is deformed to the CT images for treatment planning. This method was first validated with a prostate-phantom study. In addition, a pilot study of ten patients undergoing HDR prostate brachytherapy was conducted to test its clinical feasibility. The accuracy of their approach was assessed through the locations of three implanted fiducial (gold) markers, as well as T2-weighted MR prostate images of patients. Results: For the phantom study, the target registration error (TRE) of gold-markers was 0.41 ± 0.11 mm. For the ten patients, the TRE of gold markers was 1.18 ± 0.26 mm; the prostate volume difference between the authors’ approach and the MRI-based volume was 7.28% ± 0

  2. Registration of CT to pre-treatment MRI for planning of MR-HIFU ablation treatment of painful bone metastases

    NASA Astrophysics Data System (ADS)

    Noorda, Yolanda H.; Bartels, Lambertus W.; Huisman, Merel; Nijenhuis, Robbert J.; AAJ van den Bosch, Maurice; Pluim, Josien PW

    2014-08-01

    MR-HIFU is a new non-invasive treatment modality that can be used for palliation in patients with painful bone metastases. Since treatment strategies are mainly focused on the ablation of periosteal nerves, information on the presence and geometry of cortical bone influences the treatment strategy, both in determining the acoustic power and in avoiding safety issues related to far-field heating. Although MRI is available for imaging during treatment, CT is best used for examining the cortical bone. We present a registration method for registering CT and MR images of patients with bone metastases prior to therapy. CT and MRI data were obtained from nine patients with metastatic bone lesions at varying locations. A two-step registration approach was used, performing simultaneous rigid registration of all available MR images in the first step and an affine and deformable registration with an additional bone metric in the second step. The performance was evaluated using landmark annotation by clinical observers. An average registration error of 4.5 mm was obtained, which was comparable to the slice thickness of the data. The performance of the registration algorithm was satisfactory, even with differences in MRI acquisition parameters and for various anatomical sites. The obtained CT overlay is useful for treatment planning, as it allows an assessment of the integrity of the cortical bone. CT-MR registration is therefore recommended for HIFU treatment planning of patients with bone metastases.

  3. Earth Science Imagery Registration

    NASA Technical Reports Server (NTRS)

    LeMoigne, Jacqueline; Morisette, Jeffrey; Cole-Rhodes, Arlene; Johnson, Kisha; Netanyahu, Nathan S.; Eastman, Roger; Stone, Harold; Zavorin, Ilya

    2003-01-01

    The study of global environmental changes involves the comparison, fusion, and integration of multiple types of remotely-sensed data at various temporal, radiometric, and spatial resolutions. Results of this integration may be utilized for global change analysis, as well as for the validation of new instruments or for new data analysis. Furthermore, future multiple satellite missions will include many different sensors carried on separate platforms, and the amount of remote sensing data to be combined is increasing tremendously. For all of these applications, the first required step is fast and automatic image registration, and as this need for automating registration techniques is being recognized, it becomes necessary to survey all the registration methods which may be applicable to Earth and space science problems and to evaluate their performances on a large variety of existing remote sensing data as well as on simulated data of soon-to-be-flown instruments. In this paper we present one of the first steps toward such an exhaustive quantitative evaluation. First, the different components of image registration algorithms are reviewed, and different choices for each of these components are described. Then, the results of the evaluation of the corresponding algorithms combining these components are presented o n several datasets. The algorithms are based on gray levels or wavelet features and compute rigid transformations (including scale, rotation, and shifts). Test datasets include synthetic data as well as data acquired over several EOS Land Validation Core Sites with the IKONOS and the Landsat-7 sensors.

  4. A Framework for Linear and Non-Linear Registration of Diffusion-Weighted MRIs Using Angular Interpolation

    PubMed Central

    Duarte-Carvajalino, Julio M.; Sapiro, Guillermo; Harel, Noam; Lenglet, Christophe

    2013-01-01

    Registration of diffusion-weighted magnetic resonance images (DW-MRIs) is a key step for population studies, or construction of brain atlases, among other important tasks. Given the high dimensionality of the data, registration is usually performed by relying on scalar representative images, such as the fractional anisotropy (FA) and non-diffusion-weighted (b0) images, thereby ignoring much of the directional information conveyed by DW-MR datasets itself. Alternatively, model-based registration algorithms have been proposed to exploit information on the preferred fiber orientation(s) at each voxel. Models such as the diffusion tensor or orientation distribution function (ODF) have been used for this purpose. Tensor-based registration methods rely on a model that does not completely capture the information contained in DW-MRIs, and largely depends on the accurate estimation of tensors. ODF-based approaches are more recent and computationally challenging, but also better describe complex fiber configurations thereby potentially improving the accuracy of DW-MRI registration. A new algorithm based on angular interpolation of the diffusion-weighted volumes was proposed for affine registration, and does not rely on any specific local diffusion model. In this work, we first extensively compare the performance of registration algorithms based on (i) angular interpolation, (ii) non-diffusion-weighted scalar volume (b0), and (iii) diffusion tensor image (DTI). Moreover, we generalize the concept of angular interpolation (AI) to non-linear image registration, and implement it in the FMRIB Software Library (FSL). We demonstrate that AI registration of DW-MRIs is a powerful alternative to volume and tensor-based approaches. In particular, we show that AI improves the registration accuracy in many cases over existing state-of-the-art algorithms, while providing registered raw DW-MRI data, which can be used for any subsequent analysis. PMID:23596381

  5. Robust rigid registration of retinal angiograms through optimization.

    PubMed

    Dréo, Johann; Nunes, Jean-Claude; Siarry, Patrick

    2006-12-01

    Retinal fundus photographs are employed as standard diagnostic tools in ophthalmology. Serial photographs of the flow of fluorescein and indocyanine green (ICG) dye are used to determine the areas of the retinal lesions. For objective measurements of features, the registration of the images is a necessity. In this paper, we employ optimization techniques for registration with the help of 2-parameter translational motion model of retinal angiograms, based on non-linear pre-processing (Wiener filtering and morphological gradient) and computation of the similarity criteria for the alignment of the two gradient images for any given rigid transformation. The optimization methods are effectively employed to minimize the similarity criterion. The presence of noise, the variations in the background and the temporal variation of the fluorescence level pose serious problems in obtaining a robust registration of the retinal images. Moreover, local search strategies are not robust in the case of ICG angiograms, even if one uses a multiresolution approach. The present work makes a systematic comparison of different optimization techniques, namely the minimization method derived from the optical flow formulation, the Nelder-Mead local search and the HCIAC ant colony metaheuristic, each optimizing a similarity criterion for the gradient images. The impact of the resolution and median filtering of gradient image is studied and the robustness of the approaches is tested through experimental studies, performed on macular fluorescein and ICG angiographies. Our proposed optimization techniques have shown interesting results especially for high resolution difficult registration problems. Moreover, this approach seems promising for affine (6-parameter motion model) or elastical registrations. PMID:17034991

  6. A New Method for Navigating Optimal Direction for Pulling Ligand from Binding Pocket: Application to Ranking Binding Affinity by Steered Molecular Dynamics.

    PubMed

    Vuong, Quan Van; Nguyen, Tin Trung; Li, Mai Suan

    2015-12-28

    In this paper we present a new method for finding the optimal path for pulling a ligand from the binding pocket using steered molecular dynamics (SMD). Scoring function is defined as the steric hindrance caused by a receptor to ligand movement. Then the optimal path corresponds to the minimum of this scoring function. We call the new method MSH (Minimal Steric Hindrance). Contrary to existing navigation methods, our approach takes into account the geometry of the ligand while other methods including CAVER only consider the ligand as a sphere with a given radius. Using three different target + receptor sets, we have shown that the rupture force Fmax and nonequilibrium work Wpull obtained based on the MSH method show a much higher correlation with experimental data on binding free energies compared to CAVER. Furthermore, Wpull was found to be a better indicator for binding affinity than Fmax. Thus, the new MSH method is a reliable tool for obtaining the best direction for ligand exiting from the binding site. Its combination with the standard SMD technique can provide reasonable results for ranking binding affinities using Wpull as a scoring function. PMID:26595261

  7. Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure-based modeling methods

    SciTech Connect

    Politi, Regina; Rusyn, Ivan; Tropsha, Alexander

    2014-10-01

    The thyroid hormone receptor (THR) is an important member of the nuclear receptor family that can be activated by endocrine disrupting chemicals (EDC). Quantitative Structure–Activity Relationship (QSAR) models have been developed to facilitate the prioritization of THR-mediated EDC for the experimental validation. The largest database of binding affinities available at the time of the study for ligand binding domain (LBD) of THRβ was assembled to generate both continuous and classification QSAR models with an external accuracy of R{sup 2} = 0.55 and CCR = 0.76, respectively. In addition, for the first time a QSAR model was developed to predict binding affinities of antagonists inhibiting the interaction of coactivators with the AF-2 domain of THRβ (R{sup 2} = 0.70). Furthermore, molecular docking studies were performed for a set of THRβ ligands (57 agonists and 15 antagonists of LBD, 210 antagonists of the AF-2 domain, supplemented by putative decoys/non-binders) using several THRβ structures retrieved from the Protein Data Bank. We found that two agonist-bound THRβ conformations could effectively discriminate their corresponding ligands from presumed non-binders. Moreover, one of the agonist conformations could discriminate agonists from antagonists. Finally, we have conducted virtual screening of a chemical library compiled by the EPA as part of the Tox21 program to identify potential THRβ-mediated EDCs using both QSAR models and docking. We concluded that the library is unlikely to have any EDC that would bind to the THRβ. Models developed in this study can be employed either to identify environmental chemicals interacting with the THR or, conversely, to eliminate the THR-mediated mechanism of action for chemicals of concern. - Highlights: • This is the largest curated dataset for ligand binding domain (LBD) of the THRβ. • We report the first QSAR model for antagonists of AF-2 domain of THRβ. • A combination of QSAR and docking enables

  8. A new usage of ASIFT for the range image registration

    NASA Astrophysics Data System (ADS)

    Liu, Chun-Yang; Li, Dong; Tian, Jin-Dong

    2014-11-01

    This paper addresses the range image registration problem for views having overlapping area and which may include substantial noise. The current state of the art in range image registration is best represented by the well-known iterative closest point (ICP) algorithm and numerous variations on it. Although this method is effective in many domains, it nevertheless suffers from two key limitations: It requires prealignment of the range surfaces to a reasonable starting point and it is not robust to outliers arising either from noise or low surface overlap. This paper proposes a new approach that avoids these problems for precision range image registration, by using a new, robust method based on ASIFT followed by ICP. Up to now, this approach has been evaluated by experiment. We define the fitness function to calculate the time for the convergence stage of ICP, because the time required is very important. ASIFT are capable of image matching even when there is fully affine variant. The novel ICP search algorithm we present following ASIFT offers much faster convergence than prior ICP methods, and ensures more precise alignments, even in the presence of significant noise, than mean squared error or other well-known robust cost functions.

  9. Affinity Purification Method for the Identification of Nonribosomal Peptide Biosynthetic Enzymes Using a Synthetic Probe for Adenylation Domains.

    PubMed

    Ishikawa, Fumihiro; Kakeya, Hideaki

    2016-01-01

    A series of inhibitors have been designed based on 5'-O-sulfamoyl adenosine (AMS) that display tight binding characteristics towards the inhibition of adenylation (A) domains in nonribosomal peptide synthetases (NRPSs). We recently developed an affinity probe for A domains that could be used to facilitate the specific isolation and identification of NRPS modules. Our synthetic probe, which is a biotinylated variant of L-Phe-AMS (L-Phe-AMS-biotin), selectively targets the A domains in NRPS modules that recognize and convert L-Phe to an aminoacyl adenylate in whole proteomes. In this chapter, we describe the design and synthesis of L-Phe-AMS-biotin and provide a summary of our work towards the development of a series of protocols for the specific enrichment of NRPS modules using this probe. PMID:26831701

  10. A novel user classification method for femtocell network by using affinity propagation algorithm and artificial neural network.

    PubMed

    Ahmed, Afaz Uddin; Islam, Mohammad Tariqul; Ismail, Mahamod; Kibria, Salehin; Arshad, Haslina

    2014-01-01

    An artificial neural network (ANN) and affinity propagation (AP) algorithm based user categorization technique is presented. The proposed algorithm is designed for closed access femtocell network. ANN is used for user classification process and AP algorithm is used to optimize the ANN training process. AP selects the best possible training samples for faster ANN training cycle. The users are distinguished by using the difference of received signal strength in a multielement femtocell device. A previously developed directive microstrip antenna is used to configure the femtocell device. Simulation results show that, for a particular house pattern, the categorization technique without AP algorithm takes 5 indoor users and 10 outdoor users to attain an error-free operation. While integrating AP algorithm with ANN, the system takes 60% less training samples reducing the training time up to 50%. This procedure makes the femtocell more effective for closed access operation. PMID:25133214

  11. Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure based modeling methods

    PubMed Central

    Politi, Regina; Rusyn, Ivan; Tropsha, Alexander

    2016-01-01

    The thyroid hormone receptor (THR) is an important member of the nuclear receptor family that can be activated by endocrine disrupting chemicals (EDC). Quantitative Structure-Activity Relationship (QSAR) models have been developed to facilitate the prioritization of THR-mediated EDC for the experimental validation. The largest database of binding affinities available at the time of the study for ligand binding domain (LBD) of THRβ was assembled to generate both continuous and classification QSAR models with an external accuracy of R2=0.55 and CCR=0.76, respectively. In addition, for the first time a QSAR model was developed to predict binding affinities of antagonists inhibiting the interaction of coactivators with the AF-2 domain of THRβ (R2=0.70). Furthermore, molecular docking studies were performed for a set of THRβ ligands (57 agonists and 15 antagonists of LBD, 210 antagonists of the AF-2 domain, supplemented by putative decoys/non-binders) using several THRβ structures retrieved from the Protein Data Bank. We found that two agonist-bound THRβ conformations could effectively discriminate their corresponding ligands from presumed non-binders. Moreover, one of the agonist conformations could discriminate agonists from antagonists. Finally, we have conducted virtual screening of a chemical library compiled by the EPA as part of the Tox21 program to identify potential THRβ-mediated EDCs using both QSAR models and docking. We concluded that the library is unlikely to have any EDC that would bind to the THRβ. Models developed in this study can be employed either to identify environmental chemicals interacting with the THR or, conversely, to eliminate the THR-mediated mechanism of action for chemicals of concern. PMID:25058446

  12. A novel thiol-affinity micropipette tip method using zinc(II)-cyclen-attached agarose beads for enrichment of cysteine-containing molecules.

    PubMed

    Kusamoto, Hiroshi; Shiba, Akio; Koretake, Norinao; Fujioka, Haruto; Hieda, Yuhzo; Kinoshita-Kikuta, Emiko; Kinoshita, Eiji; Koike, Tohru

    2016-09-15

    Cysteine-containing biomolecules are attractive targets in the study of thiol biology. Here we introduce a novel method for the selective enrichment of thiol-containing molecules using a thiol-capture zinc(II) complex of 1,4,7,10-tetraazacyclododecane (Zn(2+)-cyclen). Recognition of N-acetylcysteine amide by Zn(2+)-cyclen has been studied by potentiometric pH titration, revealing formation of a 1:1 thiolate-bound Zn(2+)-cyclen complex with a large thiolate-affinity constant of 10(6.2)M(-1) at 25°C and I=0.10M (NaCl). The Zn(2+)-bound thiolate anion is unexpectedly stable in aqueous solution at pH 7.8 under atmospheric conditions for a few days. These findings have contributed to the development of a convenient method for separation of thiol compounds by using a micropipette tip. A 200μL micropipette tip containing 10μL of hydrophilic cross-linked agarose beads attached to Zn(2+)-cyclen moieties was prepared. All steps for thiol-affinity separation (binding, washing, and eluting) are conducted using aqueous buffers at room temperature. The entire separation protocol requires less than 15min per sample. We demonstrate practical example separations of cysteine-containing molecules. This micropipette tip method would be used preferentially as an alternative to existing tools for reliable enrichment of thiol-containing molecules. PMID:27498090

  13. Affine hypersurfaces with parallel difference tensor relative to affine α-connection

    NASA Astrophysics Data System (ADS)

    Li, Cece

    2014-12-01

    Li and Zhang (2014) studied affine hypersurfaces of R n + 1 with parallel difference tensor relative to the affine α-connection ∇ (α), and characterized the generalized Cayley hypersurfaces by K n - 1 ≠ 0 and ∇ (α) K = 0 for some nonzero constant α, where the affine α-connection ∇ (α) of information geometry was introduced on affine hypersurface. In this paper, by a slightly different method we continue to study affine hypersurfaces with ∇ (α) K = 0, if α = 0 we further assume that the Pick invariant vanishes and affine metric is of constant sectional curvature. It is proved that they are either hyperquadrics or improper affine hypersphere with flat indefinite affine metric, the latter can be locally given as a graph of a polynomial of at most degree n + 1 with constant Hessian determinant. In particular, if the affine metric is definite, Lorentzian, or its negative index is 2, we complete the classification of such hypersurfaces.

  14. Probability Density Estimation Using Isocontours and Isosurfaces: Application to Information-Theoretic Image Registration

    PubMed Central

    Rajwade, Ajit; Banerjee, Arunava; Rangarajan, Anand

    2010-01-01

    We present a new geometric approach for determining the probability density of the intensity values in an image. We drop the notion of an image as a set of discrete pixels and assume a piecewise-continuous representation. The probability density can then be regarded as being proportional to the area between two nearby isocontours of the image surface. Our paper extends this idea to joint densities of image pairs. We demonstrate the application of our method to affine registration between two or more images using information-theoretic measures such as mutual information. We show cases where our method outperforms existing methods such as simple histograms, histograms with partial volume interpolation, Parzen windows, etc., under fine intensity quantization for affine image registration under significant image noise. Furthermore, we demonstrate results on simultaneous registration of multiple images, as well as for pairs of volume data sets, and show some theoretical properties of our density estimator. Our approach requires the selection of only an image interpolant. The method neither requires any kind of kernel functions (as in Parzen windows), which are unrelated to the structure of the image in itself, nor does it rely on any form of sampling for density estimation. PMID:19147876

  15. Intervertebral anticollision constraints improve out-of-plane translation accuracy of a single-plane fluoroscopy-to-CT registration method for measuring spinal motion

    SciTech Connect

    Lin, Cheng-Chung; Tsai, Tsung-Yuan; Hsu, Shih-Jung; Lu, Tung-Wu; Shih, Ting-Fang; Wang, Ting-Ming

    2013-03-15

    Purpose: The study aimed to propose a new single-plane fluoroscopy-to-CT registration method integrated with intervertebral anticollision constraints for measuring three-dimensional (3D) intervertebral kinematics of the spine; and to evaluate the performance of the method without anticollision and with three variations of the anticollision constraints via an in vitro experiment. Methods: The proposed fluoroscopy-to-CT registration approach, called the weighted edge-matching with anticollision (WEMAC) method, was based on the integration of geometrical anticollision constraints for adjacent vertebrae and the weighted edge-matching score (WEMS) method that matched the digitally reconstructed radiographs of the CT models of the vertebrae and the measured single-plane fluoroscopy images. Three variations of the anticollision constraints, namely, T-DOF, R-DOF, and A-DOF methods, were proposed. An in vitro experiment using four porcine cervical spines in different postures was performed to evaluate the performance of the WEMS and the WEMAC methods. Results: The WEMS method gave high precision and small bias in all components for both vertebral pose and intervertebral pose measurements, except for relatively large errors for the out-of-plane translation component. The WEMAC method successfully reduced the out-of-plane translation errors for intervertebral kinematic measurements while keeping the measurement accuracies for the other five degrees of freedom (DOF) more or less unaltered. The means (standard deviations) of the out-of-plane translational errors were less than -0.5 (0.6) and -0.3 (0.8) mm for the T-DOF method and the R-DOF method, respectively. Conclusions: The proposed single-plane fluoroscopy-to-CT registration method reduced the out-of-plane translation errors for intervertebral kinematic measurements while keeping the measurement accuracies for the other five DOF more or less unaltered. With the submillimeter and subdegree accuracy, the WEMAC method was

  16. Improved method for the on-line metal chelate affinity chromatography-high-performance liquid chromatographic determination of tetracycline antibiotics in animal products.

    PubMed

    Cooper, A D; Stubbings, G W; Kelly, M; Tarbin, J A; Farrington, W H; Shearer, G

    1998-07-01

    An improved on-line metal chelate affinity chromatography-high-performance liquid chromatography (MCAC-HPLC) method for the determination of tetracycline antibiotics in animal tissues and egg has been developed. Extraction was carried out with ethyl acetate. The extract was then evaporated to dryness and reconstituted in methanol prior to on-line MCAC clean-up and HPLC-UV determination. Recoveries of tetracycline, oxytetracycline, demeclocycline and chlortetracycline in the range 42% to 101% were obtained from egg, poultry, fish and venison tissues spiked at 25 micrograms kg-1. Limits of detection less than 10 microgram kg-1 were estimated for all four analytes. This method has higher throughput, higher recovery and lower limits of detection than a previously reported on-line MCAC-HPLC method which involved aqueous extraction and solid-phase extraction clean-up. PMID:9691328

  17. Interactive multigrid refinement for deformable image registration.

    PubMed

    Zhou, Wu; Xie, Yaoqin

    2013-01-01

    Deformable image registration is the spatial mapping of corresponding locations between images and can be used for important applications in radiotherapy. Although numerous methods have attempted to register deformable medical images automatically, such as salient-feature-based registration (SFBR), free-form deformation (FFD), and demons, no automatic method for registration is perfect, and no generic automatic algorithm has shown to work properly for clinical applications due to the fact that the deformation field is often complex and cannot be estimated well by current automatic deformable registration methods. This paper focuses on how to revise registration results interactively for deformable image registration. We can manually revise the transformed image locally in a hierarchical multigrid manner to make the transformed image register well with the reference image. The proposed method is based on multilevel B-spline to interactively revise the deformable transformation in the overlapping region between the reference image and the transformed image. The resulting deformation controls the shape of the transformed image and produces a nice registration or improves the registration results of other registration methods. Experimental results in clinical medical images for adaptive radiotherapy demonstrated the effectiveness of the proposed method. PMID:24232828

  18. A survey of medical image registration - under review.

    PubMed

    Viergever, Max A; Maintz, J B Antoine; Klein, Stefan; Murphy, Keelin; Staring, Marius; Pluim, Josien P W

    2016-10-01

    A retrospective view on the past two decades of the field of medical image registration is presented, guided by the article "A survey of medical image registration" (Maintz and Viergever, 1998). It shows that the classification of the field introduced in that article is still usable, although some modifications to do justice to advances in the field would be due. The main changes over the last twenty years are the shift from extrinsic to intrinsic registration, the primacy of intensity-based registration, the breakthrough of nonlinear registration, the progress of inter-subject registration, and the availability of generic image registration software packages. Two problems that were called urgent already 20 years ago, are even more urgent nowadays: Validation of registration methods, and translation of results of image registration research to clinical practice. It may be concluded that the field of medical image registration has evolved, but still is in need of further development in various aspects. PMID:27427472

  19. DEFORMABLE REGISTRATION OF MACULAR OCT USING A-MODE SCAN SIMILARITY

    PubMed Central

    Chen, Min; Lang, Andrew; Sotirchos, Elias; Ying, Howard S.; Calabresi, Peter A.; Prince, Jerry L.; Carass, Aaron

    2013-01-01

    Optical coherence tomography (OCT) of the macular cube has become an increasingly important tool for investigating and managing retinal pathology. One important new area of investigation is the analysis of anatomic variably across a population. Such an analysis on the retina requires the construction of a normalized space, which is generally created through deformable registration of each subject into a common template. Unfortunately, state-of-the-art 3D registration tools fail to adequately spatially normalize retinal OCT images. This work proposes a new deformable registration algorithm for OCT images using the similarity between pairs of A-mode scans. First, a retinal OCT specific affine step is presented, which uses automated landmarks to perform global translations and individual rescaling of all the subject’s A-mode scans. Then, a deformable registration using regularized one-dimensional radial basis functions is applied to further align the retinal layers. Results on 15 subjects show the improved accuracy of this approach in comparison to state of the art methods with respect to registration for labeling. Additional results show the ability to generate stereotaxic spaces for retinal OCT. PMID:24443687

  20. Retinal image registration via feature-guided Gaussian mixture model.

    PubMed

    Liu, Chengyin; Ma, Jiayi; Ma, Yong; Huang, Jun

    2016-07-01

    Registration of retinal images taken at different times, from different perspectives, or with different modalities is a critical prerequisite for the diagnoses and treatments of various eye diseases. This problem can be formulated as registration of two sets of sparse feature points extracted from the given images, and it is typically solved by first creating a set of putative correspondences and then removing the false matches as well as estimating the spatial transformation between the image pairs or solved by estimating the correspondence and transformation jointly involving an iteration process. However, the former strategy suffers from missing true correspondences, and the latter strategy does not make full use of local appearance information, which may be problematic for low-quality retinal images due to a lack of reliable features. In this paper, we propose a feature-guided Gaussian mixture model (GMM) to address these issues. We formulate point registration as the estimation of a feature-guided mixture of densities: A GMM is fitted to one point set, such that both the centers and local features of the Gaussian densities are constrained to coincide with the other point set. The problem is solved under a unified maximum-likelihood framework together with an iterative expectation-maximization algorithm initialized by the confident feature correspondences, where the image transformation is modeled by an affine function. Extensive experiments on various retinal images show the robustness of our approach, which consistently outperforms other state-of-the-art methods, especially when the data is badly degraded. PMID:27409682

  1. A volumetric model-based 2D to 3D registration method for measuring kinematics of natural knees with single-plane fluoroscopy

    SciTech Connect

    Tsai, Tsung-Yuan; Lu, Tung-Wu; Chen, Chung-Ming; Kuo, Mei-Ying; Hsu, Horng-Chaung

    2010-03-15

    Purpose: Accurate measurement of the three-dimensional (3D) rigid body and surface kinematics of the natural human knee is essential for many clinical applications. Existing techniques are limited either in their accuracy or lack more realistic experimental evaluation of the measurement errors. The purposes of the study were to develop a volumetric model-based 2D to 3D registration method, called the weighted edge-matching score (WEMS) method, for measuring natural knee kinematics with single-plane fluoroscopy to determine experimentally the measurement errors and to compare its performance with that of pattern intensity (PI) and gradient difference (GD) methods. Methods: The WEMS method gives higher priority to matching of longer edges of the digitally reconstructed radiograph and fluoroscopic images. The measurement errors of the methods were evaluated based on a human cadaveric knee at 11 flexion positions. Results: The accuracy of the WEMS method was determined experimentally to be less than 0.77 mm for the in-plane translations, 3.06 mm for out-of-plane translation, and 1.13 deg. for all rotations, which is better than that of the PI and GD methods. Conclusions: A new volumetric model-based 2D to 3D registration method has been developed for measuring 3D in vivo kinematics of natural knee joints with single-plane fluoroscopy. With the equipment used in the current study, the accuracy of the WEMS method is considered acceptable for the measurement of the 3D kinematics of the natural knee in clinical applications.

  2. DR-BUDDI (Diffeomorphic Registration for Blip-Up blip-Down Diffusion Imaging) Method for Correcting Echo Planar Imaging Distortions

    PubMed Central

    Irfanoglu, M. Okan; Modi, Pooja; Nayak, Amritha; Hutchinson, Elizabeth B.; Sarlls, Joelle; Pierpaoli, Carlo

    2014-01-01

    We propose an echo planar imaging (EPI) distortion correction method (DR-BUDDI), specialized for diffusion MRI, which uses data acquired twice with reversed phase encoding directions, often referred to as blip-up blip-down acquisitions. DR-BUDDI can incorporate information from an undistorted structural MRI and also use diffusion-weighted images (DWI) to guide the registration, improving the quality of the registration in the presence of large deformations and in white matter regions. DR-BUDDI does not require the transformations for correcting blip-up and blip-down images to be the exact inverse of each other. Imposing the theoretical “blip-up blip-down distortion symmetry” may not be appropriate in the presence of common clinical scanning artifacts such as motion, ghosting, Gibbs ringing, vibrations, and low signal-to-noise. The performance of DR-BUDDI is evaluated with several data sets and compared to other existing blip-up blip-down correction approaches. The proposed method is robust and generally outperforms existing approaches. The inclusion of the DWIs in the correction process proves to be very important to obtain a reliable correction of distortions in the brain stem. Methods that do not use DWIs may produce a visually appealing correction of the non-diffusion weighted b = 0 s/mm2 images, but the directionally encoded color maps computed from the tensor reveal an abnormal anatomy of the white matter pathways. PMID:25433212

  3. Bi-modal imaging of atherosclerotic plaques: Automated method for co-registration between fluorescence lifetime imaging and intravascular ultrasound data

    NASA Astrophysics Data System (ADS)

    Gorpas, Dimitris; Fatakdawala, Hussain; Bec, Julien; Ma, Dinglong; Yankelevich, Diego R.; Bishop, John W.; Qi, Jinyi; Marcu, Laura

    2014-03-01

    The risk of atherosclerosis plaque rupture cannot be assessed by the current imaging systems and thus new multi-modal technologies are under investigation. This includes combining a new fluorescence lifetime imaging (FLIm) technique, which is sensitive to plaque biochemical features, with conventional intravascular ultrasound (IVUS), which provides information on plaque morphology. In this study we present an automated method allowing for the co-registration of imaging data acquired based on these two techniques. Intraluminal studies were conducted in ex-vivo segments of human coronaries with a multimodal catheter integrating a commercial IVUS (40 MHz) and a rotational side-viewing fiber based multispectral FLIm system (355 nm excitation, 390+/-20, 452+/-22 and 542+/-25 nm acquisition wavelengths). The proposed method relies on the lumen/intima boundary extraction from the IVUS polar images. Image restoration is applied for the noise reduction and edge enhancement, while gray-scale peak tracing over the A-lines of the IVUS polar images is applied for the lumen boundary extraction. The detection of the guide-wire artifact is used for the angular registration between FLIm and IVUS data, after which the lifetime values can be mapped onto the segmented lumen/intima interface. The segmentation accuracy has been assessed against manual tracings, providing 0.120+/-0.054 mm mean Hausdorff distance. This method makes the bi-modal FLIm and IVUS approach feasible for comprehensive intravascular diagnostic by providing co-registered biochemical and morphological information about atherosclerotic plaques.

  4. A simple nonradioactive method for the determination of the binding affinities of antibodies induced by hapten bioconjugates for drugs of abuse.

    PubMed

    Torres, Oscar B; Antoline, Joshua F G; Li, Fuying; Jalah, Rashmi; Jacobson, Arthur E; Rice, Kenner C; Alving, Carl R; Matyas, Gary R

    2016-02-01

    The accurate analytical measurement of binding affinities of polyclonal antibody in sera to heroin, 6-acetylmorphine (6-AM), and morphine has been a challenging task. A simple nonradioactive method that uses deuterium-labeled drug tracers and equilibrium dialysis (ED) combined with ultra performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) to measure the apparent dissociation constant (K d) of antibodies to 6-AM and morphine is described. The method can readily detect antibodies with K d in the low nanomolar range. Since heroin is rapidly degraded in sera, esterase inhibitors were included in the assay, greatly reducing heroin hydrolysis. MS/MS detection directly measured the heroin in the assay after overnight ED, thereby allowing the quantitation of % bound heroin in lieu of K d as an alternative measurement to assess heroin binding to polyclonal antibody sera. This is the first report that utilizes a solution-based assay to quantify heroin-antibody binding without being confounded by the presence of 6-AM and morphine and to measure K d of polyclonal antibody to 6-AM. Hapten surrogates 6-AcMorHap, 6-PrOxyHap, MorHap, DiAmHap, and DiPrOxyHap coupled to tetanus toxoid (TT) were used to generate high affinity antibodies to heroin, 6-AM, and morphine. In comparison to competition ED-UPLC/MS/MS which gave K d values in the nanomolar range, the commonly used competition enzyme-linked immunosorbent assay (ELISA) measured the 50% inhibition concentration (IC50) values in the micromolar range. Despite the differences in K d and IC50 values, similar trends in affinities of hapten antibodies to heroin, 6-AM, and morphine were observed by both methods. Competition ED-UPLC/MS/MS revealed that among the five TT-hapten bioconjugates, TT-6-AcMorHap and TT-6-PrOxyHap induced antibodies that bound heroin, 6-AM, and morphine. In contrast, TT-MorHap induced antibodies that poorly bound heroin, while TT-DiAmHap and TT-DiPrOxyHap induced antibodies either did not

  5. Deformable registration for image-guided spine surgery: preserving rigid body vertebral morphology in free-form transformations

    NASA Astrophysics Data System (ADS)

    Reaungamornrat, S.; Wang, A. S.; Uneri, A.; Otake, Y.; Zhao, Z.; Khanna, A. J.; Siewerdsen, J. H.

    2014-03-01

    Purpose: Deformable registration of preoperative and intraoperative images facilitates accurate localization of target and critical anatomy in image-guided spine surgery. However, conventional deformable registration fails to preserve the morphology of rigid bone anatomy and can impart distortions that confound high-precision intervention. We propose a constrained registration method that preserves rigid morphology while allowing deformation of surrounding soft tissues. Method: The registration method aligns preoperative 3D CT to intraoperative cone-beam CT (CBCT) using free-form deformation (FFD) with penalties on rigid body motion imposed according to a simple intensity threshold. The penalties enforced 3 properties of a rigid transformation - namely, constraints on affinity (AC), orthogonality (OC), and properness (PC). The method also incorporated an injectivity constraint (IC) to preserve topology. Physical experiments (involving phantoms, an ovine spine, and a human cadaver) as well as digital simulations were performed to evaluate the sensitivity to registration parameters, preservation of rigid body morphology, and overall registration accuracy of constrained FFD in comparison to conventional unconstrained FFD (denoted uFFD) and Demons registration. Result: FFD with orthogonality and injectivity constraints (denoted FFD+OC+IC) demonstrated improved performance compared to uFFD and Demons. Affinity and properness constraints offered little or no additional improvement. The FFD+OC+IC method preserved rigid body morphology at near-ideal values of zero dilatation (D = 0.05, compared to 0.39 and 0.56 for uFFD and Demons, respectively) and shear (S = 0.08, compared to 0.36 and 0.44 for uFFD and Demons, respectively). Target registration error (TRE) was similarly improved for FFD+OC+IC (0.7 mm), compared to 1.4 and 1.8 mm for uFFD and Demons. Results were validated in human cadaver studies using CT and CBCT images, with FFD+OC+IC providing excellent preservation

  6. Consistency-based rectification of nonrigid registrations

    PubMed Central

    Gass, Tobias; Székely, Gábor; Goksel, Orcun

    2015-01-01

    Abstract. We present a technique to rectify nonrigid registrations by improving their group-wise consistency, which is a widely used unsupervised measure to assess pair-wise registration quality. While pair-wise registration methods cannot guarantee any group-wise consistency, group-wise approaches typically enforce perfect consistency by registering all images to a common reference. However, errors in individual registrations to the reference then propagate, distorting the mean and accumulating in the pair-wise registrations inferred via the reference. Furthermore, the assumption that perfect correspondences exist is not always true, e.g., for interpatient registration. The proposed consistency-based registration rectification (CBRR) method addresses these issues by minimizing the group-wise inconsistency of all pair-wise registrations using a regularized least-squares algorithm. The regularization controls the adherence to the original registration, which is additionally weighted by the local postregistration similarity. This allows CBRR to adaptively improve consistency while locally preserving accurate pair-wise registrations. We show that the resulting registrations are not only more consistent, but also have lower average transformation error when compared to known transformations in simulated data. On clinical data, we show improvements of up to 50% target registration error in breathing motion estimation from four-dimensional MRI and improvements in atlas-based segmentation quality of up to 65% in terms of mean surface distance in three-dimensional (3-D) CT. Such improvement was observed consistently using different registration algorithms, dimensionality (two-dimensional/3-D), and modalities (MRI/CT). PMID:26158083

  7. Effect of Registration on Cyclical Kinematic Data

    PubMed Central

    Crane, Elizabeth A.; Cassidy, Ruth B.; Rothman, Edward D.; Gerstner, Geoffrey E.

    2010-01-01

    Given growing interest in Functional Data Analysis (FDA) as a useful method for analyzing human movement data, it is critical to understand the effects of standard FDA procedures, including registration, on biomechanical analyses. Registration is used to reduce phase variability between curves while preserving the individual curves shape and amplitude. The application of three methods available to assess registration could benefit those in the biomechanics community using FDA techniques: comparison of mean curves, comparison of average RMS values, and assessment of time-warping functions. Therefore, the present study has two purposes. First, the necessity of registration applied to cyclical data after time normalization is assessed. Second, we illustrate the three methods for evaluating registration effects. Masticatory jaw movements of 22 healthy adults (2 males, 21 females) were tracked while subjects chewed a gum-based pellet for 20 seconds. Motion data were captured at 60 Hz with two gen-locked video cameras. Individual chewing cycles were time normalized and then transformed into functional observations. Registration did not affect mean curves and warping functions were linear. Although registration decreased the RMS, indicating a decrease in inter-subject variability, the difference was not statistically significant. Together these results indicate that registration may not always be necessary for cyclical chewing data. An important contribution of this paper is the illustration of three methods for evaluating registration that are easy to apply and useful for judging whether the extra data manipulation is necessary. PMID:20537335

  8. Assessment of artery dilation by using image registration based on spatial features

    NASA Astrophysics Data System (ADS)

    Oubel, Estanislao; Neemuchwala, Huzefa; Hero, Alfred; Boisrobert, Loic; Laclaustra, Martin; Frangi, Alejandro F.

    2005-04-01

    The use of affine image registration based on normalized mutual information (NMI) has recently been proposed by Frangi et al. as an automatic method for assessing brachial artery flow mediated dilation (FMD) for the characterization of endothelial function. Even though this method solves many problems of previous approaches, there are still some situations that can lead to misregistration between frames, such as the presence of adjacent vessels due to probe movement, muscle fibres or poor image quality. Despite its widespread use as a registration metric and its promising results, MI is not the panacea and can occasionally fail. Previous work has attempted to include spatial information into the image similarity metric. Among these methods the direct estimation of alpha-MI through Minimum Euclidean Graphs allows to include spatial information and it seems suitable to tackle the registration problem in vascular images, where well oriented structures corresponding to vessel walls and muscle fibres are present. The purpose of this work is twofold. Firstly, we aim to evaluate the effect of including spatial information in the performance of the method suggested by Frangi et al. by using alpha-MI of spatial features as similarity metric. Secondly, the application of image registration to long image sequences in which both rigid motion and deformation are present will be used as a benchmark to prove the value of alpha-MI as a similarity metric, and will also allow us to make a comparative study with respect to NMI.

  9. Coronary CT angiography (cCTA): automated registration of coronary arterial trees from multiple phases.

    PubMed

    Hadjiiski, Lubomir; Zhou, Chuan; Chan, Heang-Ping; Chughtai, Aamer; Agarwal, Prachi; Kuriakose, Jean; Kazerooni, Ella; Wei, Jun; Patel, Smita

    2014-08-21

    Coronary computed tomography angiography (cCTA) is a commonly used imaging modality for the evaluation of coronary artery disease. cCTA is generally reconstructed in multiple cardiac phases because different coronary arteries may be better visualized in some phases than in others due to the periodic cardiac motion. We are developing an automated registration method for coronary arterial trees from multiple-phase cCTA that has potential application in building a 'best-quality' tree to facilitate image analysis and detection of stenotic plaques. Given the segmented left or right coronary arterial (LCA or RCA) trees from the multiple phases as input, the adjacent phase pairs, where displacements are relatively small, are registered by a specifically designed method based on a cubic B-spline with fast localized optimization (CBSO). For the phase pairs with large displacements, a global registration using an affine transform with quadratic terms and nonlinear simplex optimization (AQSO) is followed by a local registration using CBSO to refine the AQSO registered volumes. 26 LCA and 26 RCA trees with six cCTA phases from 26 patients were used for registration evaluation. The average distances for the tree pairs between the adjacent phases with small displacements before and after CBSO registration were 0.96  ±  0.79 and 0.76  ±  0.61 mm respectively for LCA, and 0.93  ±  0.97 and 0.64  ±  0.43 mm, respectively for RCA. The average distance differences before and after registration were statistically significant (p < 0.001) for both LCA and RCA trees. The average distances for the distant phases with large displacements before registration, after AQSO registration, and finally after the CBSO registration were 2.85  ±  1.46, 1.62  ±  0.76, and 0.97  ±  0.43 mm, respectively for LCA, and 4.03  ±  2.36, 2.18  ±  1.11, and 0.97  ±  0.44 mm, respectively for RCA. The average distance differences

  10. Coronary CT angiography (cCTA): automated registration of coronary arterial trees from multiple phases

    NASA Astrophysics Data System (ADS)

    Hadjiiski, Lubomir; Zhou, Chuan; Chan, Heang-Ping; Chughtai, Aamer; Agarwal, Prachi; Kuriakose, Jean; Kazerooni, Ella; Wei, Jun; Patel, Smita

    2014-08-01

    Coronary computed tomography angiography (cCTA) is a commonly used imaging modality for the evaluation of coronary artery disease. cCTA is generally reconstructed in multiple cardiac phases because different coronary arteries may be better visualized in some phases than in others due to the periodic cardiac motion. We are developing an automated registration method for coronary arterial trees from multiple-phase cCTA that has potential application in building a ‘best-quality’ tree to facilitate image analysis and detection of stenotic plaques. Given the segmented left or right coronary arterial (LCA or RCA) trees from the multiple phases as input, the adjacent phase pairs, where displacements are relatively small, are registered by a specifically designed method based on a cubic B-spline with fast localized optimization (CBSO). For the phase pairs with large displacements, a global registration using an affine transform with quadratic terms and nonlinear simplex optimization (AQSO) is followed by a local registration using CBSO to refine the AQSO registered volumes. 26 LCA and 26 RCA trees with six cCTA phases from 26 patients were used for registration evaluation. The average distances for the tree pairs between the adjacent phases with small displacements before and after CBSO registration were 0.96  ±  0.79 and 0.76  ±  0.61 mm respectively for LCA, and 0.93  ±  0.97 and 0.64  ±  0.43 mm, respectively for RCA. The average distance differences before and after registration were statistically significant (p < 0.001) for both LCA and RCA trees. The average distances for the distant phases with large displacements before registration, after AQSO registration, and finally after the CBSO registration were 2.85  ±  1.46, 1.62  ±  0.76, and 0.97  ±  0.43 mm, respectively for LCA, and 4.03  ±  2.36, 2.18  ±  1.11, and 0.97  ±  0.44 mm, respectively for RCA. The average distance differences between every two

  11. Deformable medical image registration of pleural cavity for photodynamic therapy by using finite-element based method

    NASA Astrophysics Data System (ADS)

    Penjweini, Rozhin; Kim, Michele M.; Dimofte, Andrea; Finlay, Jarod C.; Zhu, Timothy C.

    2016-03-01

    When the pleural cavity is opened during the surgery portion of pleural photodynamic therapy (PDT) of malignant mesothelioma, the pleural volume will deform. This impacts the delivered dose when using highly conformal treatment techniques. To track the anatomical changes and contour the lung and chest cavity, an infrared camera-based navigation system (NDI) is used during PDT. In the same patient, a series of computed tomography (CT) scans of the lungs are also acquired before the surgery. The reconstructed three-dimensional contours from both NDI and CTs are imported into COMSOL Multiphysics software, where a finite element-based (FEM) deformable image registration is obtained. The CT contour is registered to the corresponding NDI contour by overlapping the center of masses and aligning their orientations. The NDI contour is considered as the reference contour, and the CT contour is used as the target one, which will be deformed. Deformed Geometry model is applied in COMSOL to obtain a deformed target contour. The distortion of the volume at X, Y and Z is mapped to illustrate the transformation of the target contour. The initial assessment shows that FEM-based image deformable registration can fuse images acquired by different modalities. It provides insights into the deformation of anatomical structures along X, Y and Z-axes. The deformed contour has good matches to the reference contour after the dynamic matching process. The resulting three-dimensional deformation map can be used to obtain the locations of other critical anatomic structures, e.g., heart, during surgery.

  12. Deformable medical image registration of pleural cavity for photodynamic therapy by using finite-element based method

    PubMed Central

    Penjweini, Rozhin; Kim, Michele M.; Dimofte, Andrea; Finlay, Jarod C; Zhu, Timothy C.

    2016-01-01

    When the pleural cavity is opened during the surgery portion of pleural photodynamic therapy (PDT) of malignant mesothelioma, the pleural volume will deform. This impacts the delivered dose when using highly conformal treatment techniques. To track the anatomical changes and contour the lung and chest cavity, an infrared camera–based navigation system (NDI) is used during PDT. In the same patient, a series of computed tomography (CT) scans of the lungs are also acquired before the surgery. The reconstructed three-dimensional contours from both NDI and CTs are imported into COMSOL Multiphysics software, where a finite element-based (FEM) deformable image registration is obtained. The CT contour is registered to the corresponding NDI contour by overlapping the center of masses and aligning their orientations. The NDI contour is considered as the reference contour, and the CT contour is used as the target one, which will be deformed. Deformed Geometry model is applied in COMSOL to obtain a deformed target contour. The distortion of the volume at X, Y and Z is mapped to illustrate the transformation of the target contour. The initial assessment shows that FEM-based image deformable registration can fuse images acquired by different modalities. It provides insights into the deformation of anatomical structures along X, Y and Z-axes. The deformed contour has good matches to the reference contour after the dynamic matching process. The resulting three-dimensional deformation map can be used to obtain the locations of other critical anatomic structures, e.g., heart, during surgery. PMID:27053826

  13. A segmentation and point-matching enhanced efficient deformable image registration method for dose accumulation between HDR CT images

    NASA Astrophysics Data System (ADS)

    Zhen, Xin; Chen, Haibin; Yan, Hao; Zhou, Linghong; Mell, Loren K.; Yashar, Catheryn M.; Jiang, Steve; Jia, Xun; Gu, Xuejun; Cervino, Laura

    2015-04-01

    Deformable image registration (DIR) of fractional high-dose-rate (HDR) CT images is challenging due to the presence of applicators in the brachytherapy image. Point-to-point correspondence fails because of the undesired deformation vector fields (DVF) propagated from the applicator region (AR) to the surrounding tissues, which can potentially introduce significant DIR errors in dose mapping. This paper proposes a novel segmentation and point-matching enhanced efficient DIR (named SPEED) scheme to facilitate dose accumulation among HDR treatment fractions. In SPEED, a semi-automatic seed point generation approach is developed to obtain the incremented fore/background point sets to feed the random walks algorithm, which is used to segment and remove the AR, leaving empty AR cavities in the HDR CT images. A feature-based ‘thin-plate-spline robust point matching’ algorithm is then employed for AR cavity surface points matching. With the resulting mapping, a DVF defining on each voxel is estimated by B-spline approximation, which serves as the initial DVF for the subsequent Demons-based DIR between the AR-free HDR CT images. The calculated DVF via Demons combined with the initial one serve as the final DVF to map doses between HDR fractions. The segmentation and registration accuracy are quantitatively assessed by nine clinical HDR cases from three gynecological cancer patients. The quantitative analysis and visual inspection of the DIR results indicate that SPEED can suppress the impact of applicator on DIR, and accurately register HDR CT images as well as deform and add interfractional HDR doses.

  14. A segmentation and point-matching enhanced efficient deformable image registration method for dose accumulation between HDR CT images.

    PubMed

    Zhen, Xin; Chen, Haibin; Yan, Hao; Zhou, Linghong; Mell, Loren K; Yashar, Catheryn M; Jiang, Steve; Jia, Xun; Gu, Xuejun; Cervino, Laura

    2015-04-01

    Deformable image registration (DIR) of fractional high-dose-rate (HDR) CT images is challenging due to the presence of applicators in the brachytherapy image. Point-to-point correspondence fails because of the undesired deformation vector fields (DVF) propagated from the applicator region (AR) to the surrounding tissues, which can potentially introduce significant DIR errors in dose mapping. This paper proposes a novel segmentation and point-matching enhanced efficient DIR (named SPEED) scheme to facilitate dose accumulation among HDR treatment fractions. In SPEED, a semi-automatic seed point generation approach is developed to obtain the incremented fore/background point sets to feed the random walks algorithm, which is used to segment and remove the AR, leaving empty AR cavities in the HDR CT images. A feature-based 'thin-plate-spline robust point matching' algorithm is then employed for AR cavity surface points matching. With the resulting mapping, a DVF defining on each voxel is estimated by B-spline approximation, which serves as the initial DVF for the subsequent Demons-based DIR between the AR-free HDR CT images. The calculated DVF via Demons combined with the initial one serve as the final DVF to map doses between HDR fractions. The segmentation and registration accuracy are quantitatively assessed by nine clinical HDR cases from three gynecological cancer patients. The quantitative analysis and visual inspection of the DIR results indicate that SPEED can suppress the impact of applicator on DIR, and accurately register HDR CT images as well as deform and add interfractional HDR doses. PMID:25790059

  15. SU-E-J-119: What Effect Have the Volume Defined in the Alignment Clipbox for Cervical Cancer Using Automatic Registration Methods for Cone- Beam CT Verification?

    SciTech Connect

    Wang, W; Yang, H; Wang, Y; Jia, H; Xie, Y

    2014-06-01

    Purpose: To investigate the impact of different clipbox volumes with automated registration techniques using commercially available software with on board volumetric imaging(OBI) for treatment verification in cervical cancer patients. Methods: Fifty cervical cancer patients received daily CBCT scans(on-board imaging v1.5 system, Varian Medical Systems) during the first treatment week and weekly thereafter were included this analysis. A total of 450 CBCT scans were registered to the planning CTscan using pelvic clipbox(clipbox-Pelvic) and around PTV clip box(clipbox- PTV). The translations(anterior-posterior, left-right, superior-inferior) and the rotations(yaw, pitch and roll) errors for each matches were recorded. The setup errors and the systematic and random errors for both of the clip-boxes were calculated. Paired Samples t test was used to analysis the differences between clipbox-Pelvic and clipbox-PTV. Results: . The SD of systematic error(σ) was 1.0mm, 2.0mm,3.2mm and 1.9mm,2.3mm, 3.0mm in the AP, LR and SI directions for clipbox-Pelvic and clipbox-PTV, respectively. The average random error(Σ)was 1.7mm, 2.0mm,4.2mm and 1.7mm,3.4mm, 4.4mm in the AP, LR and SI directions for clipbox-Pelvic and clipbox-PTV, respectively. But, only the SI direction was acquired significantly differences between two image registration volumes(p=0.002,p=0.01 for mean and SD). For rotations, the yaw mean/SD and the pitch SD were acquired significantly differences between clipbox-Pelvic and clipbox-PTV. Conclusion: The defined volume for Image registration is important for cervical cancer when 3D/3D match was used. The alignment clipbox can effect the setup errors obtained. Further analysis is need to determine the optimal defined volume to use the image registration in cervical cancer. Conflict of interest: none.

  16. Unbiased rigid registration using transfer functions

    NASA Astrophysics Data System (ADS)

    Hahn, Dieter A.; Hornegger, Joachim; Bautz, Werner; Kuwert, Torsten; Roemer, Wolfgang

    2005-04-01

    The evaluation of tumor growth as regression under therapy is an important clinical issue. Rigid registration of sequentially acquired 3D-images has proven its value for this purpose. Existing approaches to rigid image registration use the whole volume for the estimation of the rigid transform. Non-rigid soft tissue deformation, however, will imply a bias to the registration result, because local deformations cannot be modeled by rigid transforms. Anatomical substructures, like bones or teeth, are not affected by these deformations, but follow a rigid transform. This important observation is incorporated in the proposed registration algorithm. The selection of anatomical substructure is done by manual interaction of medical experts adjusting the transfer function of the volume rendering software. The parameters of the transfer function are used to identify the voxels that are considered for registration. A rigid transform is estimated by a quaternion gradient descent algorithm based on the intensity values of the specified tissue classes. Commonly used voxel intensity measures are adjusted to the modified registration algorithm. The contribution describes the mathematical framework of the proposed registration method and its implementation in a commercial software package. The experimental evaluation includes the discussion of different similarity measures, the comparison of the proposed method to established rigid registration techniques and the evaluation of the efficiency of the new method. We conclude with the discussion of potential medical applications of the proposed registration algorithm.

  17. Morphometric affinities of gigantopithecus.

    PubMed

    Gelvin, B R

    1980-11-01

    Multivariate analyses, supplemented by univariate statistical methods, of measurements from mandibular tooth crown dimensions and the mandible of Gigantopithecus blacki, G. bilaspurensis, Plio-Plelstocene hominids, Homo erectus, and seven Neogene ape species from the genera Proconsul, Sivapithecus, Ouranopithecus, and Dryopithecus were used to assess the morphometric affinities of Gigantopithecus. The results show that Gigantopithecus displays affinities to Ouranopithecus and to the hominids, particularly the Plio-Plelstocene hominids, rather than to the apes. Ouranopithecus demonstrated dental resemblances to G. bilaspurensis and the Plio-Pleistocene hominids but mandibular similarities to the apes. Results of analyses of tooth and mandibular shape indices, combined with multivariate distance and temporal relationships, suggest that Ouranopithecus is a more likely candidate for Gigantopithecus ancestry than is Silvapithecus indicus. Shape and allometric differences between G. bilaspurensis and the robust australopithecines weaken the argument for an ancestral-descendant relationship between these groups. The results support the hypothesis that Gigantopithecus is an extinct side branch of the Hominidae. PMID:7468790

  18. Scan registration using planar features

    NASA Astrophysics Data System (ADS)

    Previtali, M.; Barazzetti, L.; Brumana, R.; Scaioni, M.

    2014-06-01

    Point cloud acquisition by using laser scanners provides an efficient way for 3D as-built modelling of indoor/outdoor urban environments. In the case of large structures, multiple scans may be required to cover the entire scene and registration is needed to merge them together. In general, the identification of corresponding geometric features among a series of scans can be used to compute the 3D rigid-body transformation useful for the registration of each scan into the reference system of the final point cloud. Different automatic or semi-automatic methods have been developed to this purpose. Several solutions based on artificial targets are available, which however may not be suitable in any situations. Methods based on surface matching (like ICP and LS3D) can be applied if the scans to align have a proper geometry and surface texture. In the case of urban and architectural scenes that present the prevalence of a few basic geometric shapes ("Legoland" scenes) the availability of many planar features is exploited here for registration. The presented technique does not require artificial targets to be added to the scanned scene. In addition, unlike other surface-based techniques (like ICP) the planar feature-based registration technique is not limited to work in a pairwise manner but it can handle the simultaneous alignment of multiple scans. Finally, some applications are presented and discussed to show how this technique can achieve accuracy comparable to a consolidated registration method.

  19. Evaluating Similarity Measures for Brain Image Registration

    PubMed Central

    Razlighi, Q. R.; Kehtarnavaz, N.; Yousefi, S.

    2013-01-01

    Evaluation of similarity measures for image registration is a challenging problem due to its complex interaction with the underlying optimization, regularization, image type and modality. We propose a single performance metric, named robustness, as part of a new evaluation method which quantifies the effectiveness of similarity measures for brain image registration while eliminating the effects of the other parts of the registration process. We show empirically that similarity measures with higher robustness are more effective in registering degraded images and are also more successful in performing intermodal image registration. Further, we introduce a new similarity measure, called normalized spatial mutual information, for 3D brain image registration whose robustness is shown to be much higher than the existing ones. Consequently, it tolerates greater image degradation and provides more consistent outcomes for intermodal brain image registration. PMID:24039378

  20. Deformable image registration with local rigidity constraints for cone-beam CT-guided spine surgery

    NASA Astrophysics Data System (ADS)

    Reaungamornrat, S.; Wang, A. S.; Uneri, A.; Otake, Y.; Khanna, A. J.; Siewerdsen, J. H.

    2014-07-01

    Image-guided spine surgery (IGSS) is associated with reduced co-morbidity and improved surgical outcome. However, precise localization of target anatomy and adjacent nerves and vessels relative to planning information (e.g., device trajectories) can be challenged by anatomical deformation. Rigid registration alone fails to account for deformation associated with changes in spine curvature, and conventional deformable registration fails to account for rigidity of the vertebrae, causing unrealistic distortions in the registered image that can confound high-precision surgery. We developed and evaluated a deformable registration method capable of preserving rigidity of bones while resolving the deformation of surrounding soft tissue. The method aligns preoperative CT to intraoperative cone-beam CT (CBCT) using free-form deformation (FFD) with constraints on rigid body motion imposed according to a simple intensity threshold of bone intensities. The constraints enforced three properties of a rigid transformation—namely, constraints on affinity (AC), orthogonality (OC), and properness (PC). The method also incorporated an injectivity constraint (IC) to preserve topology. Physical experiments involving phantoms, an ovine spine, and a human cadaver as well as digital simulations were performed to evaluate the sensitivity to registration parameters, preservation of rigid body morphology, and overall registration accuracy of constrained FFD in comparison to conventional unconstrained FFD (uFFD) and Demons registration. FFD with orthogonality and injectivity constraints (denoted FFD+OC+IC) demonstrated improved performance compared to uFFD and Demons. Affinity and properness constraints offered little or no additional improvement. The FFD+OC+IC method preserved rigid body morphology at near-ideal values of zero dilatation ({ D} = 0.05, compared to 0.39 and 0.56 for uFFD and Demons, respectively) and shear ({ S} = 0.08, compared to 0.36 and 0.44 for uFFD and Demons

  1. Deformable image registration with local rigidity constraints for cone-beam CT-guided spine surgery.

    PubMed

    Reaungamornrat, S; Wang, A S; Uneri, A; Otake, Y; Khanna, A J; Siewerdsen, J H

    2014-07-21

    Image-guided spine surgery (IGSS) is associated with reduced co-morbidity and improved surgical outcome. However, precise localization of target anatomy and adjacent nerves and vessels relative to planning information (e.g., device trajectories) can be challenged by anatomical deformation. Rigid registration alone fails to account for deformation associated with changes in spine curvature, and conventional deformable registration fails to account for rigidity of the vertebrae, causing unrealistic distortions in the registered image that can confound high-precision surgery. We developed and evaluated a deformable registration method capable of preserving rigidity of bones while resolving the deformation of surrounding soft tissue. The method aligns preoperative CT to intraoperative cone-beam CT (CBCT) using free-form deformation (FFD) with constraints on rigid body motion imposed according to a simple intensity threshold of bone intensities. The constraints enforced three properties of a rigid transformation-namely, constraints on affinity (AC), orthogonality (OC), and properness (PC). The method also incorporated an injectivity constraint (IC) to preserve topology. Physical experiments involving phantoms, an ovine spine, and a human cadaver as well as digital simulations were performed to evaluate the sensitivity to registration parameters, preservation of rigid body morphology, and overall registration accuracy of constrained FFD in comparison to conventional unconstrained FFD (uFFD) and Demons registration. FFD with orthogonality and injectivity constraints (denoted FFD+OC+IC) demonstrated improved performance compared to uFFD and Demons. Affinity and properness constraints offered little or no additional improvement. The FFD+OC+IC method preserved rigid body morphology at near-ideal values of zero dilatation (D = 0.05, compared to 0.39 and 0.56 for uFFD and Demons, respectively) and shear (S = 0.08, compared to 0.36 and 0.44 for uFFD and Demons, respectively

  2. Quantitative characterization of metastatic disease in the spine. Part I. Semiautomated segmentation using atlas-based deformable registration and the level set method

    SciTech Connect

    Hardisty, M.; Gordon, L.; Agarwal, P.; Skrinskas, T.; Whyne, C.

    2007-08-15

    Quantitative assessment of metastatic disease in bone is often considered immeasurable and, as such, patients with skeletal metastases are often excluded from clinical trials. In order to effectively quantify the impact of metastatic tumor involvement in the spine, accurate segmentation of the vertebra is required. Manual segmentation can be accurate but involves extensive and time-consuming user interaction. Potential solutions to automating segmentation of metastatically involved vertebrae are demons deformable image registration and level set methods. The purpose of this study was to develop a semiautomated method to accurately segment tumor-bearing vertebrae using the aforementioned techniques. By maintaining morphology of an atlas, the demons-level set composite algorithm was able to accurately differentiate between trans-cortical tumors and surrounding soft tissue of identical intensity. The algorithm successfully segmented both the vertebral body and trabecular centrum of tumor-involved and healthy vertebrae. This work validates our approach as equivalent in accuracy to an experienced user.

  3. Lipid Vesicle-mediated Affinity Chromatography using Magnetic Activated Cell Sorting (LIMACS): a Novel Method to Analyze Protein-lipid Interaction

    PubMed Central

    Bieberich, Erhard

    2011-01-01

    The analysis of lipid protein interaction is difficult because lipids are embedded in cell membranes and therefore, inaccessible to most purification procedures. As an alternative, lipids can be coated on flat surfaces as used for lipid ELISA and Plasmon resonance spectroscopy. However, surface coating lipids do not form microdomain structures, which may be important for the lipid binding properties. Further, these methods do not allow for the purification of larger amounts of proteins binding to their target lipids. To overcome these limitations of testing lipid protein interaction and to purify lipid binding proteins we developed a novel method termed lipid vesicle-mediated affinity chromatography using magnetic-activated cell sorting (LIMACS). In this method, lipid vesicles are prepared with the target lipid and phosphatidylserine as the anchor lipid for Annexin V MACS. Phosphatidylserine is a ubiquitous cell membrane phospholipid that shows high affinity to the protein Annexin V. Using magnetic beads conjugated to Annexin V the phosphatidylserine-containing lipid vesicles will bind to the magnetic beads. When the lipid vesicles are incubated with a cell lysate the protein binding to the target lipid will also be bound to the beads and can be co-purified using MACS. This method can also be used to test if recombinant proteins reconstitute a protein complex binding to the target lipid. We have used this method to show the interaction of atypical PKC (aPKC) with the sphingolipid ceramide and to co-purify prostate apoptosis response 4 (PAR-4), a protein binding to ceramide-associated aPKC. We have also used this method for the reconstitution of a ceramide-associated complex of recombinant aPKC with the cell polarity-related proteins Par6 and Cdc42. Since lipid vesicles can be prepared with a variety of sphingo- or phospholipids, LIMACS offers a versatile test for lipid-protein interaction in a lipid environment that resembles closely that of the cell membrane

  4. Evaluation of Mail Registration.

    ERIC Educational Resources Information Center

    San Diego Community Coll. District, CA. Research and Planning.

    The San Diego Community College District (SDCCD) implemented mail registration for all continuing students in spring 1986. In fall 1986, a comprehensive evaluation of the registration system was conducted to assess the impact of mail registration on student enrollment, to determine the impact of mailing class schedules to students' homes, to…

  5. Local image registration a comparison for bilateral registration mammography

    NASA Astrophysics Data System (ADS)

    Celaya-Padilaa, José M.; Rodriguez-Rojas, Juan; Trevino, Victor; Tamez-Pena, José G.

    2013-11-01

    Early tumor detection is key in reducing the number of breast cancer death and screening mammography is one of the most widely available and reliable method for early detection. However, it is difficult for the radiologist to process with the same attention each case, due the large amount of images to be read. Computer aided detection (CADe) systems improve tumor detection rate; but the current efficiency of these systems is not yet adequate and the correct interpretation of CADe outputs requires expert human intervention. Computer aided diagnosis systems (CADx) are being designed to improve cancer diagnosis accuracy, but they have not been efficiently applied in breast cancer. CADx efficiency can be enhanced by considering the natural mirror symmetry between the right and left breast. The objective of this work is to evaluate co-registration algorithms for the accurate alignment of the left to right breast for CADx enhancement. A set of mammograms were artificially altered to create a ground truth set to evaluate the registration efficiency of DEMONs , and SPLINE deformable registration algorithms. The registration accuracy was evaluated using mean square errors, mutual information and correlation. The results on the 132 images proved that the SPLINE deformable registration over-perform the DEMONS on mammography images.

  6. Registration of Heat Capacity Mapping Mission day and night images

    NASA Technical Reports Server (NTRS)

    Watson, K.; Hummer-Miller, S.; Sawatzky, D. L. (Principal Investigator)

    1982-01-01

    Neither iterative registration, using drainage intersection maps for control, nor cross correlation techniques were satisfactory in registering day and night HCMM imagery. A procedure was developed which registers the image pairs by selecting control points and mapping the night thermal image to the daytime thermal and reflectance images using an affine transformation on a 1300 by 1100 pixel image. The resulting image registration is accurate to better than two pixels (RMS) and does not exhibit the significant misregistration that was noted in the temperature-difference and thermal-inertia products supplied by NASA. The affine transformation was determined using simple matrix arithmetic, a step that can be performed rapidly on a minicomputer.

  7. An improved method for precise automatic co-registration of moderate and high-resolution spacecraft imagery

    NASA Technical Reports Server (NTRS)

    Bryant, Nevin A.; Logan, Thomas L.; Zobrist, Albert L.

    2006-01-01

    Improvements to the automated co-registration and change detection software package, AFIDS (Automatic Fusion of Image Data System) has recently completed development for and validation by NGA/GIAT. The improvements involve the integration of the AFIDS ultra-fine gridding technique for horizontal displacement compensation with the recently evolved use of Rational Polynomial Functions/ Coefficients (RPFs/RPCs) for image raster pixel position to Latitude/Longitude indexing. Mapping and orthorectification (correction for elevation effects) of satellite imagery defies exact projective solutions because the data are not obtained from a single point (like a camera), but as a continuous process from the orbital path. Standard image processing techniques can apply approximate solutions, but advances in the state-of-the-art had to be made for precision change-detection and time-series applications where relief offsets become a controlling factor. The earlier AFIDS procedure required the availability of a camera model and knowledge of the satellite platform ephemeredes. The recent design advances connect the spacecraft sensor Rational Polynomial Function, a deductively developed model, with the AFIDS ultrafine grid, an inductively developed representation of the relationship raster pixel position to latitude /longitude. As a result, RPCs can be updated by AFIDS, a situation often necessary due to the accuracy limits of spacecraft navigation systems. An example of precision change detection will be presented from Quickbird.

  8. Projection Registration Applied to Nondestructive Testing

    SciTech Connect

    Bingham, Philip R; Arrowood, Lloyd

    2010-01-01

    Registration of radiographic and computed tomography (CT) data has the potential to allow automated metrology and defect detection. While registration of the three-dimensional reconstructed data is a common task in the medical industry for registration of data sets from multiple detection systems, registration of projection sets has only seen development in the area of tomotherapy. Efforts in projection registration have employed a method named Fourier phase matching (FPM). This work discusses implementation and results for the application of the FPM method to industrial applications for the nondestructive testing (NDT) community. The FPM method has been implemented and modified for industrial application. Testing with simulated and experimental x-ray CT data shows excellent performance with respect to the resolution of the imaging system.

  9. Piecewise nonlinear image registration using DCT basis functions

    NASA Astrophysics Data System (ADS)

    Gan, Lin; Agam, Gady

    2015-03-01

    The deformation field in nonlinear image registration is usually modeled by a global model. Such models are often faced with the problem that a locally complex deformation cannot be accurately modeled by simply increasing degrees of freedom (DOF). In addition, highly complex models require additional regularization which is usually ineffective when applied globally. Registering locally corresponding regions addresses this problem in a divide and conquer strategy. In this paper we propose a piecewise image registration approach using Discrete Cosine Transform (DCT) basis functions for a nonlinear model. The contributions of this paper are three-folds. First, we develop a multi-level piecewise registration framework that extends the concept of piecewise linear registration and works with any nonlinear deformation model. This framework is then applied to nonlinear DCT registration. Second, we show how adaptive model complexity and regularization could be applied for local piece registration, thus accounting for higher variability. Third, we show how the proposed piecewise DCT can overcome the fundamental problem of a large curvature matrix inversion in global DCT when using high degrees of freedoms. The proposed approach can be viewed as an extension of global DCT registration where the overall model complexity is increased while achieving effective local regularization. Experimental evaluation results provide comparison of the proposed approach to piecewise linear registration using an affine transformation model and a global nonlinear registration using DCT model. Preliminary results show that the proposed approach achieves improved performance.

  10. Purification of α2-macroglobulin from Cohn Fraction IV by immobilized metal affinity chromatography: A promising method for the better utilization of plasma.

    PubMed

    Huangfu, Chaoji; Ma, Yuyuan; Lv, Maomin; Jia, Junting; Zhao, Xiong; Zhang, Jingang

    2016-07-01

    As an abundant plasma protein, α2-macroglobulin (α2-M) participates widely in physiological and pathological activities including coagulation regulation, antitumor activities, and regulation of cytokines. It also presents a therapeutic potential for radiation injury. A two-step isolation method for the purification of α2-M from Cohn Fraction IV is described. This process includes a salting-out method and immobilized metal affinity chromatography. The LC-ESI-MS/MS analysis and a comparison of the amino acid composition demonstrated that the final product was α2-M. The final protein, with a purity of approximately 95% and a yield of nearly 45%, was obtained from Cohn Fraction IV regardless of plasma haptoglobin type, although all but type 1-1 have previously been considered unfavorable for α2-M preparation. The effects of temperature, pH, and methylamine on α2-M activity were evaluated to avoid activity loss during preparation and preservation. The results suggested that α2-M activity could be readily inactivated at temperatures above 50°C, at pH levels above 9.0 or below 4.0, or in the presence of methylamine. Cohn Fraction IV is usually discarded as a biological waste product in the human serum albumin production process; because the simple process developed in this study is relatively inexpensive, the preparation of α2-M from Cohn Fraction IV may better utilize human plasma, a valuable resource. PMID:27214605

  11. Basis set limit electronic excitation energies, ionization potentials, and electron affinities for the 3d transition metal atoms: Coupled cluster and multireference methods

    NASA Astrophysics Data System (ADS)

    Balabanov, Nikolai B.; Peterson, Kirk A.

    2006-08-01

    Recently developed correlation consistent basis sets for the first row transition metal elements Sc-Zn have been utilized to determine complete basis set (CBS) scalar relativistic electron affinities, ionization potentials, and 4s23dn -2-4s1dn -1 electronic excitation energies with single reference coupled cluster methods [CCSD(T), CCSDT, and CCSDTQ] and multireference configuration interaction with three reference spaces: 3d4s, 3d4s4p, and 3d4s4p3d'. The theoretical values calculated with the highest order coupled cluster techniques at the CBS limit, including extrapolations to full configuration interaction, are well within 1kcal/mol of the corresponding experimental data. For the early transition metal elements (Sc-Mn) the internally contracted multireference averaged coupled pair functional method yielded excellent agreement with experiment; however, the atomic properties for the late transition metals (Mn-Zn) proved to be much more difficult to describe with this level of theory, even with the largest reference function of the present work.

  12. Results of automatic image registration are dependent on initial manual registration.

    PubMed

    Johnson, Joshua E; Fischer, Kenneth J

    2015-01-01

    Measurement of static alignment of articulating joints is of clinical benefit and can be determined using image-based registration. We propose a method that could potentially improve the outcome of image-based registration by using initial manual registration. Magnetic resonance images of two wrist specimens were acquired in the relaxed position and during simulated grasp. Transformations were determined from voxel-based image registration between the two volumes. The volumes were manually aligned to match as closely as possible before auto-registration, from which standard transformations were obtained. Then, translation/rotation perturbations were applied to the manual registration to obtain altered initial positions, from which altered auto-registration transformations were obtained. Models of the radiolunate joint were also constructed from the images to simulate joint contact mechanics. We compared the sensitivity of transformations (translations and rotations) and contact mechanics to altering the initial registration condition from the defined standard. We observed that with increasing perturbation, transformation errors appeared to increase and values for contact force and contact area appeared to decrease. Based on these preliminary findings, it appears that the final registration outcome is sensitive to the initial registration. PMID:25408167

  13. Registration of multitemporal low-resolution synthetic aperture radar images based on a new similarity measure

    NASA Astrophysics Data System (ADS)

    Ren, Weilong; Song, Jianshe; Zhang, Xiongmei; Cai, Xingfu

    2016-01-01

    Image registration is concerned with the precise overlap of two images. One challenging problem in this area is the registration of low-resolution synthetic aperture radar (SAR) images. In general, extracting feature points from such images is difficult due to the coarse observation and the severe speckle. The use of area similarity for image registration is another important branch to solve the problem. A similarity measure based on a conditional density function (cdf) is proposed. The cdf is specially tailored for SAR images, where the speckle is generally assumed as multiplicative gamma noise with unit mean. Additionally, a two-step procedure is devised for the registration of intro-model SAR images to improve the computational efficiency. First, the two images are roughly aligned considering only the translational difference. Then small blocks from the two images are accurately aligned and the center point of each block is treated as a control point, which is finally used to obtain the precise affine transformation between the two images. Five SAR image datasets are tested in the experiment part, and the results demonstrate the efficiency and accuracy of the proposed method.

  14. COLLINARUS: collection of image-derived non-linear attributes for registration using splines

    NASA Astrophysics Data System (ADS)

    Chappelow, Jonathan; Bloch, B. Nicolas; Rofsky, Neil; Genega, Elizabeth; Lenkinski, Robert; DeWolf, William; Viswanath, Satish; Madabhushi, Anant

    2009-02-01

    We present a new method for fully automatic non-rigid registration of multimodal imagery, including structural and functional data, that utilizes multiple texutral feature images to drive an automated spline based non-linear image registration procedure. Multimodal image registration is significantly more complicated than registration of images from the same modality or protocol on account of difficulty in quantifying similarity between different structural and functional information, and also due to possible physical deformations resulting from the data acquisition process. The COFEMI technique for feature ensemble selection and combination has been previously demonstrated to improve rigid registration performance over intensity-based MI for images of dissimilar modalities with visible intensity artifacts. Hence, we present here the natural extension of feature ensembles for driving automated non-rigid image registration in our new technique termed Collection of Image-derived Non-linear Attributes for Registration Using Splines (COLLINARUS). Qualitative and quantitative evaluation of the COLLINARUS scheme is performed on several sets of real multimodal prostate images and synthetic multiprotocol brain images. Multimodal (histology and MRI) prostate image registration is performed for 6 clinical data sets comprising a total of 21 groups of in vivo structural (T2-w) MRI, functional dynamic contrast enhanced (DCE) MRI, and ex vivo WMH images with cancer present. Our method determines a non-linear transformation to align WMH with the high resolution in vivo T2-w MRI, followed by mapping of the histopathologic cancer extent onto the T2-w MRI. The cancer extent is then mapped from T2-w MRI onto DCE-MRI using the combined non-rigid and affine transformations determined by the registration. Evaluation of prostate registration is performed by comparison with the 3 time point (3TP) representation of functional DCE data, which provides an independent estimate of cancer

  15. Rapid screening method for quinolone residues in livestock and fishery products using immobilised metal chelate affinity chromatographic clean-up and liquid chromatography-fluorescence detection.

    PubMed

    Takeda, N; Gotoh, M; Matsuoka, T

    2011-09-01

    An efficient LC method was developed for screening the presence of quinolones (QLs)--comprising fluoroquinolones (FQs) and acidic quinolones (AQs)--residues in various livestock and fishery products. Targeted analytes were for nine FQs of marbofloxacin (MAR), ofloxacin (OFL), norfloxacin (NOR), ciprofloxacin (CIP), enrofloxacin (ENR), danofloxacin (DAN), orbifloxacin (ORB), difloxacin (DIF) and sarafloxacin (SAR), and three AQs of oxolinic acid (OXA), nalidixic acid (NAL) and flumequine (FMQ). Samples comprised ten different food products covering five matrices: muscle (cattle, swine and chicken), liver (chicken), raw fish (shrimp and salmon), egg (chicken), and processed food (ham, sausage and fish sausage). This method involved a simple extraction with (1:1) acetonitrile-methanol, a highly selective clean-up with an immobilised metal chelate affinity column charged with Fe(3+), a fast isocratic LC analysis using a short column (20 mm × 4.6 mm, 3 µm) with a mobile phase of (15:85:0.1) methanol/water/formic acid, and fluorescence detection (excitation/emission wavelengths of 295 nm/455 nm for FQs (495 nm for MAR), and 320 nm/365 nm for AQs). Among FQs, pairs of NOR/OFL, ORB/DIF and ENR/DAN were incompletely resolved. A confirmatory LC run with a Mg(2+) containing methanolic mobile phase was also proposed for the samples suspected of being positive. The optimised method gave satisfactory recoveries of 88.5% (56.1-108.6%) and 78.7% (44.1-99.5%) for intra- and inter-day assays with relative standard deviations of 7.2% (0.7-18.4%) and 6.8% (1.4-16.6%), respectively. Limits of quantitation ranged from 0.8 µg kg(-1) (DAN) to 6.5 µg kg(-1) (SAR). This method was successfully employed to analyse 113 real samples and two positive samples were found: fish sausage (CIP 990 µg kg(-1)) and shrimp (ENR 20 µg kg(-1)). PMID:21749230

  16. Segmentation of three-dimensional images using non-rigid registration: methods and validation with application to confocal microscopy images of bee brains

    NASA Astrophysics Data System (ADS)

    Rohlfing, Torsten; Brandt, Robert; Menzel, Randolf; Maurer, Calvin R., Jr.

    2003-05-01

    This paper describes the application and validation of automatic segmentation of three-dimensional images by non-rigid registration to atlas images. The registration-based segmentation technique is applied to confocal microscopy images acquired from the brains of 20 bees. Each microscopy image is registered to an already segmented reference atlas image using an intensity-based non-rigid image registration algorithm. This paper evaluates and compares four different approaches: registration to an individual atlas image (IND), registration to an average shape atlas image (AVG), registration to the most similar image from a database of individual atlas images (SIM), and registration to all images from a database of individual atlas images with subsequent fuzzy segmentation (FUZ). For each strategy, the segmentation performance of the algorithm was quantified using both a global segmentation correctness measure and the similarity index. Manual segmentation of all microscopy images served as a gold standard. The best segmentation result (median correctness 91 percent of all voxels) was achieved using the FUZ paradigm. Robustness was also the best for this strategy (minimum correctness over all individuals 84 percent). The mean similarity index value of segmentations produced by the FUZ paradigm is 0.86 (IND, 0.81; AVG, 0.84; SIM, 0.82). The superiority of the FUZ paradigm is statistically significant (two-sided paired t-test, P<0.001).

  17. Robust image registration for functional magnetic resonance imaging of the brain.

    PubMed

    Hsu, C C; Wu, M T; Lee, C

    2001-09-01

    Motion-related artifacts are still a major problem in data analysis of functional magnetic resonance imaging (FMRI) studies of brain activation. However, the traditional image registration algorithm is prone to inaccuracy when there are residual variations owing to counting statistics, partial volume effects or biological variation. In particular, susceptibility artifacts usually result in remarkable signal intensity variance, and they can mislead the estimation of motion parameters. In this study, Two robust estimation algorithms for the registration of FMRI images are described. The first estimation algorithm was based on the Newton method and used Tukey's biweight objective function. The second estimation algorithm was based on the Levenberg-Marquardt technique and used a skipped mean objective function. The robust M-estimators can suppress the effects of the outliers by scaling down their error magnitudes or completely rejecting outliers using a weighting function. The proposed registration methods consisted of the following steps: fast segmentation of the brain region from noisy background as a preprocessing step; pre-registration of the volume centroids to provide a good initial estimation; and two robust estimation algorithms and a voxel sampling technique to find the affine transformation parameters. The accuracy of the algorithms was within 0.5 mm in translation and within 0.5 degrees in rotation. For the FMRI data sets, the performance of the algorithms was visually compared with the AIR 2.0 software, which is a software for image registration, using colour-coded statistical mapping by the Kolmogorov-Smirov method. Experimental results showed, that the algorithms provided significant improvement in correcting motion-related artifacts and can enhance the detection of real brain activation. PMID:11712647

  18. Image Registration Workshop Proceedings

    NASA Technical Reports Server (NTRS)

    LeMoigne, Jacqueline (Editor)

    1997-01-01

    Automatic image registration has often been considered as a preliminary step for higher-level processing, such as object recognition or data fusion. But with the unprecedented amounts of data which are being and will continue to be generated by newly developed sensors, the very topic of automatic image registration has become and important research topic. This workshop presents a collection of very high quality work which has been grouped in four main areas: (1) theoretical aspects of image registration; (2) applications to satellite imagery; (3) applications to medical imagery; and (4) image registration for computer vision research.

  19. Special Report: Affinity Chromatography.

    ERIC Educational Resources Information Center

    Parikh, Indu; Cuatrecasas, Pedro

    1985-01-01

    Describes the nature of affinity chromatography and its use in purifying enzymes, studying cell interactions, exploring hormone receptors, and other areas. The potential the technique may have in treating disease is also considered. (JN)

  20. Accuracy assessment of an automatic image-based PET/CT registration for ultrasound-guided biopsies and ablations

    NASA Astrophysics Data System (ADS)

    Kadoury, Samuel; Wood, Bradford J.; Venkatesan, Aradhana M.; Dalal, Sandeep; Xu, Sheng; Kruecker, Jochen

    2011-03-01

    The multimodal fusion of spatially tracked real-time ultrasound (US) with a prior CT scan has demonstrated clinical utility, accuracy, and positive impact upon clinical outcomes when used for guidance during biopsy and radiofrequency ablation in the treatment of cancer. Additionally, the combination of CT-guided procedures with positron emission tomography (PET) may not only enhance navigation, but add valuable information regarding the specific location and volume of the targeted masses which may be invisible on CT and US. The accuracy of this fusion depends on reliable, reproducible registration methods between PET and CT. This can avoid extensive manual efforts to correct registration which can be long and tedious in an interventional setting. In this paper, we present a registration workflow for PET/CT/US fusion by analyzing various image metrics based on normalized mutual information and cross-correlation, using both rigid and affine transformations to automatically align PET and CT. Registration is performed between the CT component of the prior PET-CT and the intra-procedural CT scan used for navigation to maximize image congruence. We evaluate the accuracy of the PET/CT registration by computing fiducial and target registration errors using anatomical landmarks and lesion locations respectively. We also report differences to gold-standard manual alignment as well as the root mean square errors for CT/US fusion. Ten patients with prior PET/CT who underwent ablation or biopsy procedures were selected for this study. Studies show that optimal results were obtained using a crosscorrelation based rigid registration with a landmark localization error of 1.1 +/- 0.7 mm using a discrete graphminimizing scheme. We demonstrate the feasibility of automated fusion of PET/CT and its suitability for multi-modality ultrasound guided navigation procedures.

  1. Post-operative assessment in Deep Brain Stimulation based on multimodal images: registration workflow and validation

    NASA Astrophysics Data System (ADS)

    Lalys, Florent; Haegelen, Claire; Abadie, Alexandre; Jannin, Pierre

    2009-02-01

    Object Movement disorders in Parkinson disease patients may require functional surgery, when medical therapy isn't effective. In Deep Brain Stimulation (DBS) electrodes are implanted within the brain to stimulate deep structures such as SubThalamic Nucleus (STN). This paper describes successive steps for constructing a digital Atlas gathering patient's location of electrodes and contacts for post operative assessment. Materials and Method 12 patients who had undergone bilateral STN DBS have participated to the study. Contacts on post-operative CT scans were automatically localized, based on black artefacts. For each patient, post operative CT images were rigidly registered to pre operative MR images. Then, pre operative MR images were registered to a MR template (super-resolution Collin27 average MRI template). This last registration was the combination of global affine, local affine and local non linear registrations, respectively. Four different studies were performed in order to validate the MR patient to template registration process, based on anatomical landmarks and clinical scores (i.e., Unified Parkinson's disease rating Scale). Visualisation software was developed for displaying into the template images the stimulated contacts represented as cylinders with a colour code related to the improvement of the UPDRS. Results The automatic contact localization algorithm was successful for all the patients. Validation studies for the registration process gave a placement error of 1.4 +/- 0.2 mm and coherence with UPDRS scores. Conclusion The developed visualization tool allows post-operative assessment for previous interventions. Correlation with additional clinical scores will certainly permit to learn more about DBS and to better understand clinical side-effects.

  2. An acousto-optical method for registration of erythrocytes' agglutination reaction—sera color influence on the resolving power

    NASA Astrophysics Data System (ADS)

    Doubrovski, V. A.; Medvedeva, M. F.; Torbin, S. O.

    2016-01-01

    The absorption spectra of agglutinating sera were used to determine blood groups. It was shown experimentally that the sera color significantly affects the resolving power of the acousto-optical method of blood typing. In order to increase the resolving power of the method and produce an invariance of the method for sera color, we suggested introducing a probing light beam individually for different sera. The proposed technique not only improves the resolving power of the method, but also reduces the risk of false interpretation of the experimental results and, hence, error in determining the blood group of the sample. The latter is especially important for the typing of blood samples with weak agglutination of erythrocytes. This study can be used in the development of an instrument for instrumental human blood group typing based on the acousto-optical method.

  3. Cadaver validation of intensity-based ultrasound to CT registration.

    PubMed

    Penney, G P; Barratt, D C; Chan, C S K; Slomczykowski, M; Carter, T J; Edwards, P J; Hawkes, D J

    2006-06-01

    A method is presented for the rigid registration of tracked B-mode ultrasound images to a CT volume of a femur and pelvis. This registration can allow tracked surgical instruments to be aligned with the CT image or an associated preoperative plan. Our method is fully automatic and requires no manual segmentation of either the ultrasound images or the CT volume. The parameter which is directly related to the speed of sound through tissue has also been included in the registration optimisation process. Experiments have been carried out on six cadaveric femurs and three cadaveric pelves. Registration results were compared with a "gold standard" registration acquired using bone implanted fiducial markers. Results show the registration method to be accurate, on average, to 1.6 mm root-mean-square target registration error. PMID:16520083

  4. Improving image segmentation by learning region affinities

    SciTech Connect

    Prasad, Lakshman; Yang, Xingwei; Latecki, Longin J

    2010-11-03

    We utilize the context information of other regions in hierarchical image segmentation to learn new regions affinities. It is well known that a single choice of quantization of an image space is highly unlikely to be a common optimal quantization level for all categories. Each level of quantization has its own benefits. Therefore, we utilize the hierarchical information among different quantizations as well as spatial proximity of their regions. The proposed affinity learning takes into account higher order relations among image regions, both local and long range relations, making it robust to instabilities and errors of the original, pairwise region affinities. Once the learnt affinities are obtained, we use a standard image segmentation algorithm to get the final segmentation. Moreover, the learnt affinities can be naturally unutilized in interactive segmentation. Experimental results on Berkeley Segmentation Dataset and MSRC Object Recognition Dataset are comparable and in some aspects better than the state-of-art methods.

  5. Deformable structure registration of bladder through surface mapping

    SciTech Connect

    Li Xiong; Viswanathan, Akila; Stewart, Alexandra J.; Haker, Steven; Tempany, Clare M.; Chin, Lee M.; Cormack, Robert A.

    2006-06-15

    Cumulative dose distributions in fractionated radiation therapy depict the dose to normal tissues and therefore may permit an estimation of the risk of normal tissue complications. However, calculation of these distributions is highly challenging because of interfractional changes in the geometry of patient anatomy. This work presents an algorithm for deformable structure registration of the bladder and the verification of the accuracy of the algorithm using phantom and patient data. In this algorithm, the registration process involves conformal mapping of genus zero surfaces using finite element analysis, and guided by three control landmarks. The registration produces a correspondence between fractions of the triangular meshes used to describe the bladder surface. For validation of the algorithm, two types of balloons were inflated gradually to three times their original size, and several computerized tomography (CT) scans were taken during the process. The registration algorithm yielded a local accuracy of 4 mm along the balloon surface. The algorithm was then applied to CT data of patients receiving fractionated high-dose-rate brachytherapy to the vaginal cuff, with the vaginal cylinder in situ. The patients' bladder filling status was intentionally different for each fraction. The three required control landmark points were identified for the bladder based on anatomy. Out of an Institutional Review Board (IRB) approved study of 20 patients, 3 had radiographically identifiable points near the bladder surface that were used for verification of the accuracy of the registration. The verification point as seen in each fraction was compared with its predicted location based on affine as well as deformable registration. Despite the variation in bladder shape and volume, the deformable registration was accurate to 5 mm, consistently outperforming the affine registration. We conclude that the structure registration algorithm presented works with reasonable accuracy and

  6. Affinity Proteomics in the mountains: Alpbach 2015.

    PubMed

    Taussig, Michael J

    2016-09-25

    The 2015 Alpbach Workshop on Affinity Proteomics, organised by the EU AFFINOMICS consortium, was the 7th workshop in this series. As in previous years, the focus of the event was the current state of affinity methods for proteome analysis, including complementarity with mass spectrometry, progress in recombinant binder production methods, alternatives to classical antibodies as affinity reagents, analysis of proteome targets, industry focus on biomarkers, and diagnostic and clinical applications. The combination of excellent science with Austrian mountain scenery and winter sports engender an atmosphere that makes this series of workshops exceptional. The articles in this Special Issue represent a cross-section of the presentations at the 2015 meeting. PMID:27118167

  7. Automatic registration and alignment on a template of cardiac stress and rest reoriented SPECT images.

    PubMed

    Declerck, J; Feldmar, J; Goris, M L; Betting, F

    1997-12-01

    Single photon emission computed tomography (SPECT) imaging with 201Tl or 99mTc agent is used to assess the location or the extent of myocardial infarction or ischemia. A method is proposed to decrease the effect of operator variability in the visual or quantitative interpretation of scintigraphic myocardial perfusion studies. To effect this, the patient's myocardial images (target cases) are registered automatically over a template image, utilizing a nonrigid transformation. The intermediate steps are: 1) Extraction of feature points in both stress and rest three-dimensional (3-D) images. The images are resampled in a polar geometry to detect edge points, which in turn are filtered by the use of a priori constraints. The remaining feature points are assumed to be points on the edges of the left ventricular myocardium. 2) Registration of stress and rest images with a global affine transformation. The matching method is an adaptation of the iterative closest point algorithm. 3) Registration and morphological matching of both stress and rest images on a template using a nonrigid local spline transformation following a global affine transformation. 4) Resampling of both stress and rest images in the geometry of the template. Optimization of the method was performed on a database of 40 pairs of stress and rest images selected to obtain a wide variation of images and abnormalities. Further testing was performed on 250 cases selected from the same database on the basis of the availability of angiographic results and patient stratification. PMID:9533574

  8. An ITK implementation of a physics-based non-rigid registration method for brain deformation in image-guided neurosurgery

    PubMed Central

    Liu, Yixun; Kot, Andriy; Drakopoulos, Fotis; Yao, Chengjun; Fedorov, Andriy; Enquobahrie, Andinet; Clatz, Olivier; Chrisochoides, Nikos P.

    2014-01-01

    As part of the ITK v4 project efforts, we have developed ITK filters for physics-based non-rigid registration (PBNRR), which satisfies the following requirements: account for tissue properties in the registration, improve accuracy compared to rigid registration, and reduce execution time using GPU and multi-core accelerators. The implementation has three main components: (1) Feature Point Selection, (2) Block Matching (mapped to both multi-core and GPU processors), and (3) a Robust Finite Element Solver. The use of multi-core and GPU accelerators in ITK v4 provides substantial performance improvements. For example, for the non-rigid registration of brain MRIs, the performance of the block matching filter on average is about 10 times faster when 12 hyperthreaded multi-cores are used and about 83 times faster when the NVIDIA Tesla GPU is used in Dell Workstation. PMID:24778613

  9. Registration and Marking Requirements for UAS. Unmanned Aircraft System (UAS) Registration

    NASA Technical Reports Server (NTRS)

    2005-01-01

    The registration of an aircraft is a prerequisite for issuance of a U.S. certificate of airworthiness by the FAA. The procedures and requirements for aircraft registration, and the subsequent issuance of registration numbers, are contained in FAR Part 47. However, the process/method(s) for applying the requirements of Parts 45 & 47 to Unmanned Aircraft Systems (UAS) has not been defined. This task resolved the application of 14 CFR Parts 45 and 47 to UAS. Key Findings: UAS are aircraft systems and as such the recommended approach to registration is to follow the same process for registration as manned aircraft. This will require manufacturers to comply with the requirements for 14 CFR 47, Aircraft Registration and 14 CFR 45, Identification and Registration Marking. In addition, only the UA should be identified with the N number registration markings. There should also be a documentation link showing the applicability of the control station and communication link to the UA. The documentation link can be in the form of a Type Certificate Data Sheet (TCDS) entry or a UAS logbook entry. The recommended process for the registration of UAS is similar to the manned aircraft process and is outlined in a 6-step process in the paper.

  10. DIRBoost-an algorithm for boosting deformable image registration: application to lung CT intra-subject registration.

    PubMed

    Muenzing, Sascha E A; van Ginneken, Bram; Viergever, Max A; Pluim, Josien P W

    2014-04-01

    We introduce a boosting algorithm to improve on existing methods for deformable image registration (DIR). The proposed DIRBoost algorithm is inspired by the theory on hypothesis boosting, well known in the field of machine learning. DIRBoost utilizes a method for automatic registration error detection to obtain estimates of local registration quality. All areas detected as erroneously registered are subjected to boosting, i.e. undergo iterative registrations by employing boosting masks on both the fixed and moving image. We validated the DIRBoost algorithm on three different DIR methods (ANTS gSyn, NiftyReg, and DROP) on three independent reference datasets of pulmonary image scan pairs. DIRBoost reduced registration errors significantly and consistently on all reference datasets for each DIR algorithm, yielding an improvement of the registration accuracy by 5-34% depending on the dataset and the registration algorithm employed. PMID:24556079

  11. Immobilized metal ion affinity partitioning, a method combining metal-protein interaction and partitioning of proteins in aqueous two-phase systems.

    PubMed

    Birkenmeier, G; Vijayalakshmi, M A; Stigbrand, T; Kopperschläger, G

    1991-02-22

    Immobilized metal ions were used for the affinity extraction of proteins in aqueous two-phase systems composed of polyethylene glycol (PEG) and dextran or PEG and salt. Soluble chelating polymers were prepared by covalent attachment of metal-chelating groups to PEG. The effect on the partitioning of proteins of such chelating PEG derivatives coordinated with different metal ions is demonstrated. The proteins studied were alpha 2-macroglobulin, tissue plasminogen activator, superoxide dismutase and monoclonal antibodies. The results indicate that immobilized metal ion affinity partitioning provides excellent potential for the extraction of proteins. PMID:1710621

  12. Adaptive deformable image registration of inhomogeneous tissues

    NASA Astrophysics Data System (ADS)

    Ren, Jing

    2015-03-01

    Physics based deformable registration can provide physically consistent image match of deformable soft tissues. In order to help radiologist/surgeons to determine the status of malicious tumors, we often need to accurately align the regions with embedded tumors. This is a very challenging task since the tumor and the surrounding tissues have very different tissue properties such as stiffness and elasticity. In order to address this problem, based on minimum strain energy principle in elasticity theory, we propose to partition the whole region of interest into smaller sub-regions and dynamically adjust weights of vessel segments and bifurcation points in each sub-region in the registration objective function. Our previously proposed fast vessel registration is used as a component in the inner loop. We have validated the proposed method using liver MR images from human subjects. The results show that our method can detect the large registration errors and improve the registration accuracy in the neighborhood of the tumors and guarantee the registration errors to be within acceptable accuracy. The proposed technique has the potential to significantly improve the registration capability and the quality of clinical diagnosis and treatment planning.

  13. A Multistage Approach for Image Registration.

    PubMed

    Bowen, Francis; Hu, Jianghai; Du, Eliza Yingzi

    2016-09-01

    Successful image registration is an important step for object recognition, target detection, remote sensing, multimodal content fusion, scene blending, and disaster assessment and management. The geometric and photometric variations between images adversely affect the ability for an algorithm to estimate the transformation parameters that relate the two images. Local deformations, lighting conditions, object obstructions, and perspective differences all contribute to the challenges faced by traditional registration techniques. In this paper, a novel multistage registration approach is proposed that is resilient to view point differences, image content variations, and lighting conditions. Robust registration is realized through the utilization of a novel region descriptor which couples with the spatial and texture characteristics of invariant feature points. The proposed region descriptor is exploited in a multistage approach. A multistage process allows the utilization of the graph-based descriptor in many scenarios thus allowing the algorithm to be applied to a broader set of images. Each successive stage of the registration technique is evaluated through an effective similarity metric which determines subsequent action. The registration of aerial and street view images from pre- and post-disaster provide strong evidence that the proposed method estimates more accurate global transformation parameters than traditional feature-based methods. Experimental results show the robustness and accuracy of the proposed multistage image registration methodology. PMID:26292357

  14. Automatic visible and infrared face registration based on silhouette matching and robust transformation estimation

    NASA Astrophysics Data System (ADS)

    Tian, Tian; Mei, Xiaoguang; Yu, Yang; Zhang, Can; Zhang, Xiaoye

    2015-03-01

    Registration of multi-sensor data (particularly visible color sensors and infrared sensors) is a prerequisite for multimodal image analysis such as image fusion. In this paper, we proposed an automatic registration technique for visible and infrared face images based on silhouette matching and robust transformation estimation. The key idea is to represent a (visible or infrared) face image by its silhouette which is extracted from the image's edge map and consists of a set of discrete points, and then align the two silhouette point sets by using their feature similarity and spatial geometrical information. More precisely, our algorithm first matches the silhouette point sets by their local shape features such as shape context, which creates a set of putative correspondences that may contaminated by outliers. Next, we estimate the accurate transformation from the putative correspondence set under a robust maximum likelihood framework combining with the EM algorithm, where the transformation between the image pair is modeled by a parametric model such as the rigid or affine transformation. The qualitative and quantitative comparisons on a publicly available database demonstrate that our method significantly outperforms other state-of-the-art visible/infrared face registration methods. As a result, our method will be beneficial for fusion-based face recognition.

  15. Fast musculoskeletal registration based on shape matching.

    PubMed

    Gilles, Benjamin; Pai, Dinesh K

    2008-01-01

    This paper presents a new method for computing elastic and plastic deformations in the context of discrete deformable model-based registration. Internal forces are estimated by averaging local transforms between reference and current particle positions. Our technique can accommodate large non-linear deformations, and is unconditionally stable. Moreover, it is simple to implement and versatile. We show how to tune model stiffness and computational cost, which is important for efficient registration, and demonstrate our technique in the complex problem of inter-patient musculoskeletal registration. PMID:18982681

  16. Registration of multi-view apical 3D echocardiography images

    NASA Astrophysics Data System (ADS)

    Mulder, H. W.; van Stralen, M.; van der Zwaan, H. B.; Leung, K. Y. E.; Bosch, J. G.; Pluim, J. P. W.

    2011-03-01

    Real-time three-dimensional echocardiography (RT3DE) is a non-invasive method to visualize the heart. Disadvantageously, it suffers from non-uniform image quality and a limited field of view. Image quality can be improved by fusion of multiple echocardiography images. Successful registration of the images is essential for prosperous fusion. Therefore, this study examines the performance of different methods for intrasubject registration of multi-view apical RT3DE images. A total of 14 data sets was annotated by two observers who indicated the position of the apex and four points on the mitral valve ring. These annotations were used to evaluate registration. Multi-view end-diastolic (ED) as well as end-systolic (ES) images were rigidly registered in a multi-resolution strategy. The performance of single-frame and multi-frame registration was examined. Multi-frame registration optimizes the metric for several time frames simultaneously. Furthermore, the suitability of mutual information (MI) as similarity measure was compared to normalized cross-correlation (NCC). For initialization of the registration, a transformation that describes the probe movement was obtained by manually registering five representative data sets. It was found that multi-frame registration can improve registration results with respect to single-frame registration. Additionally, NCC outperformed MI as similarity measure. If NCC was optimized in a multi-frame registration strategy including ED and ES time frames, the performance of the automatic method was comparable to that of manual registration. In conclusion, automatic registration of RT3DE images performs as good as manual registration. As registration precedes image fusion, this method can contribute to improved quality of echocardiography images.

  17. Performance Evaluation of Automatic Anatomy Segmentation Algorithm on Repeat or Four-Dimensional Computed Tomography Images Using Deformable Image Registration Method

    SciTech Connect

    Wang He; Garden, Adam S.; Zhang Lifei; Wei Xiong; Ahamad, Anesa; Kuban, Deborah A.; Komaki, Ritsuko; O'Daniel, Jennifer; Zhang Yongbin; Mohan, Radhe; Dong Lei

    2008-09-01

    Purpose: Auto-propagation of anatomic regions of interest from the planning computed tomography (CT) scan to the daily CT is an essential step in image-guided adaptive radiotherapy. The goal of this study was to quantitatively evaluate the performance of the algorithm in typical clinical applications. Methods and Materials: We had previously adopted an image intensity-based deformable registration algorithm to find the correspondence between two images. In the present study, the regions of interest delineated on the planning CT image were mapped onto daily CT or four-dimensional CT images using the same transformation. Postprocessing methods, such as boundary smoothing and modification, were used to enhance the robustness of the algorithm. Auto-propagated contours for 8 head-and-neck cancer patients with a total of 100 repeat CT scans, 1 prostate patient with 24 repeat CT scans, and 9 lung cancer patients with a total of 90 four-dimensional CT images were evaluated against physician-drawn contours and physician-modified deformed contours using the volume overlap index and mean absolute surface-to-surface distance. Results: The deformed contours were reasonably well matched with the daily anatomy on the repeat CT images. The volume overlap index and mean absolute surface-to-surface distance was 83% and 1.3 mm, respectively, compared with the independently drawn contours. Better agreement (>97% and <0.4 mm) was achieved if the physician was only asked to correct the deformed contours. The algorithm was also robust in the presence of random noise in the image. Conclusion: The deformable algorithm might be an effective method to propagate the planning regions of interest to subsequent CT images of changed anatomy, although a final review by physicians is highly recommended.

  18. Optimized Affinity Capture of Yeast Protein Complexes.

    PubMed

    LaCava, John; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Rout, Michael P

    2016-01-01

    Here, we describe an affinity isolation protocol. It uses cryomilled yeast cell powder for producing cell extracts and antibody-conjugated paramagnetic beads for affinity capture. Guidelines for determining the optimal extraction solvent composition are provided. Captured proteins are eluted in a denaturing solvent (sodium dodecyl sulfate polyacrylamide gel electrophoresis sample buffer) for gel-based proteomic analyses. Although the procedures can be modified to use other sources of cell extract and other forms of affinity media, to date we have consistently obtained the best results with the method presented. PMID:27371596

  19. Aptamers in Affinity Separations: Stationary Separation

    NASA Astrophysics Data System (ADS)

    Ravelet, Corinne; Peyrin, Eric

    The use of DNA or RNA aptamers as tools in analytical chemistry is a very promising field of research because of their capabilities to bind specifically the target molecules with an affinity similar to that of antibodies. Notably, they appear to be of great interest as target-specific ligands for the separation and capture of various analytes in affinity chromatography and related affinity-based methods such as magnetic bead technology. In this chapter, the recent developments of these aptamer-based separation/capture approaches are addressed.

  20. Affinity purification of heme-tagged proteins.

    PubMed

    Asher, Wesley B; Bren, Kara L

    2014-01-01

    Protein affinity purification techniques are widely used for isolating pure target proteins for biochemical and structural characterization. Herein, we describe the protocol for affinity-based purification of proteins expressed in Escherichia coli that uses the coordination of a peptide tag covalently modified with heme c, known as a heme-tag, to an L-histidine immobilized Sepharose resin. This approach provides an affinity purification tag visible to the eye, facilitating tracking of the protein. In addition, we describe methods for specifically detecting heme-tagged proteins in SDS-PAGE gels using a heme-staining procedure and for quantifying the proteins using a pyridine hemochrome assay. PMID:24943311

  1. Deformable Medical Image Registration: A Survey

    PubMed Central

    Sotiras, Aristeidis; Davatzikos, Christos; Paragios, Nikos

    2013-01-01

    Deformable image registration is a fundamental task in medical image processing. Among its most important applications, one may cite: i) multi-modality fusion, where information acquired by different imaging devices or protocols is fused to facilitate diagnosis and treatment planning; ii) longitudinal studies, where temporal structural or anatomical changes are investigated; and iii) population modeling and statistical atlases used to study normal anatomical variability. In this paper, we attempt to give an overview of deformable registration methods, putting emphasis on the most recent advances in the domain. Additional emphasis has been given to techniques applied to medical images. In order to study image registration methods in depth, their main components are identified and studied independently. The most recent techniques are presented in a systematic fashion. The contribution of this paper is to provide an extensive account of registration techniques in a systematic manner. PMID:23739795

  2. Evaluation of five image registration tools for abdominal CT: pitfalls and opportunities with soft anatomy

    NASA Astrophysics Data System (ADS)

    Lee, Christopher P.; Xu, Zhoubing; Burke, Ryan P.; Baucom, Rebeccah; Poulose, Benjamin K.; Abramson, Richard G.; Landman, Bennett A.

    2015-03-01

    Image registration has become an essential image processing technique to compare data across time and individuals. With the successes in volumetric brain registration, general-purpose software tools are beginning to be applied to abdominal computed tomography (CT) scans. Herein, we evaluate five current tools for registering clinically acquired abdominal CT scans. Twelve abdominal organs were labeled on a set of 20 atlases to enable assessment of correspondence. The 20 atlases were pairwise registered based on only intensity information with five registration tools (affine IRTK, FNIRT, Non-Rigid IRTK, NiftyReg, and ANTs). Following the brain literature, the Dice similarity coefficient (DSC), mean surface distance, and Hausdorff distance were calculated on the registered organs individually. However, interpretation was confounded due to a significant proportion of outliers. Examining the retrospectively selected top 1 and 5 atlases for each target revealed that there was a substantive performance difference between methods. To further our understanding, we constructed majority vote segmentation with the top 5 DSC values for each organ and target. The results illustrated a median improvement of 85% in DSC between the raw results and majority vote. These experiments show that some images may be well registered to some targets using the available software tools, but there is significant room for improvement and reveals the need for innovation and research in the field of registration in abdominal CTs. If image registration is to be used for local interpretation of abdominal CT, great care must be taken to account for outliers (e.g., atlas selection in statistical fusion).

  3. SU-E-J-209: Verification of 3D Surface Registration Between Stereograms and CT Images

    SciTech Connect

    Han, T; Gifford, K; Smith, B; Salehpour, M

    2014-06-01

    Purpose: Stereography can provide a visualization of the skin surface for radiation therapy patients. The aim of this study was to verify the registration algorithm in a commercial image analysis software, 3dMDVultus, for the fusion of stereograms and CT images. Methods: CT and stereographic scans were acquired of a head phantom and a deformable phantom. CT images were imported in 3dMDVultus and the surface contours were generated by threshold segmentation. Stereograms were reconstructed in 3dMDVultus. The resulting surfaces were registered with Vultus algorithm and then exported to in-house registration software and compared with four algorithms: rigid, affine, non-rigid iterative closest point (ICP) and b-spline algorithm. RMS (root-mean-square residuals of the surface point distances) error between the registered CT and stereogram surfaces was calculated and analyzed. Results: For the head phantom, the maximum RMS error between registered CT surfaces to stereogram was 6.6 mm for Vultus algorithm, whereas the mean RMS error was 0.7 mm. For the deformable phantom, the maximum RMS error was 16.2 mm for Vultus algorithm, whereas the mean RMS error was 4.4 mm. Non-rigid ICP demonstrated the best registration accuracy, as the mean of RMS errors were both within 1 mm. Conclusion: The accuracy of registration algorithm in 3dMDVultus was verified and exceeded RMS of 2 mm for deformable cases. Non-rigid ICP and b-spline algorithms improve the registration accuracy for both phantoms, especially in deformable one. For those patients whose body habitus deforms during radiation therapy, more advanced nonrigid algorithms need to be used.

  4. A Method for 3D Histopathology Reconstruction Supporting Mouse Microvasculature Analysis.

    PubMed

    Xu, Yiwen; Pickering, J Geoffrey; Nong, Zengxuan; Gibson, Eli; Arpino, John-Michael; Yin, Hao; Ward, Aaron D

    2015-01-01

    Structural abnormalities of the microvasculature can impair perfusion and function. Conventional histology provides good spatial resolution with which to evaluate the microvascular structure but affords no 3-dimensional information; this limitation could lead to misinterpretations of the complex microvessel network in health and disease. The objective of this study was to develop and evaluate an accurate, fully automated 3D histology reconstruction method to visualize the arterioles and venules within the mouse hind-limb. Sections of the tibialis anterior muscle from C57BL/J6 mice (both normal and subjected to femoral artery excision) were reconstructed using pairwise rigid and affine registrations of 5 µm-thick, paraffin-embedded serial sections digitized at 0.25 µm/pixel. Low-resolution intensity-based rigid registration was used to initialize the nucleus landmark-based registration, and conventional high-resolution intensity-based registration method. The affine nucleus landmark-based registration was developed in this work and was compared to the conventional affine high-resolution intensity-based registration method. Target registration errors were measured between adjacent tissue sections (pairwise error), as well as with respect to a 3D reference reconstruction (accumulated error, to capture propagation of error through the stack of sections). Accumulated error measures were lower (p < 0.01) for the nucleus landmark technique and superior vasculature continuity was observed. These findings indicate that registration based on automatic extraction and correspondence of small, homologous landmarks may support accurate 3D histology reconstruction. This technique avoids the otherwise problematic "banana-into-cylinder" effect observed using conventional methods that optimize the pairwise alignment of salient structures, forcing them to be section-orthogonal. This approach will provide a valuable tool for high-accuracy 3D histology tissue reconstructions for

  5. TU-B-19A-01: Image Registration II: TG132-Quality Assurance for Image Registration

    SciTech Connect

    Brock, K; Mutic, S

    2014-06-15

    AAPM Task Group 132 was charged with a review of the current approaches and solutions for image registration in radiotherapy and to provide recommendations for quality assurance and quality control of these clinical processes. As the results of image registration are always used as the input of another process for planning or delivery, it is important for the user to understand and document the uncertainty associate with the algorithm in general and the Result of a specific registration. The recommendations of this task group, which at the time of abstract submission are currently being reviewed by the AAPM, include the following components. The user should understand the basic image registration techniques and methods of visualizing image fusion. The disclosure of basic components of the image registration by commercial vendors is critical in this respect. The physicists should perform end-to-end tests of imaging, registration, and planning/treatment systems if image registration is performed on a stand-alone system. A comprehensive commissioning process should be performed and documented by the physicist prior to clinical use of the system. As documentation is important to the safe implementation of this process, a request and report system should be integrated into the clinical workflow. Finally, a patient specific QA practice should be established for efficient evaluation of image registration results. The implementation of these recommendations will be described and illustrated during this educational session. Learning Objectives: Highlight the importance of understanding the image registration techniques used in their clinic. Describe the end-to-end tests needed for stand-alone registration systems. Illustrate a comprehensive commissioning program using both phantom data and clinical images. Describe a request and report system to ensure communication and documentation. Demonstrate an clinically-efficient patient QA practice for efficient evaluation of image

  6. Ensemble learning incorporating uncertain registration.

    PubMed

    Simpson, Ivor J A; Woolrich, Mark W; Andersson, Jesper L R; Groves, Adrian R; Schnabel, Julia A

    2013-04-01

    This paper proposes a novel approach for improving the accuracy of statistical prediction methods in spatially normalized analysis. This is achieved by incorporating registration uncertainty into an ensemble learning scheme. A probabilistic registration method is used to estimate a distribution of probable mappings between subject and atlas space. This allows the estimation of the distribution of spatially normalized feature data, e.g., grey matter probability maps. From this distribution, samples are drawn for use as training examples. This allows the creation of multiple predictors, which are subsequently combined using an ensemble learning approach. Furthermore, extra testing samples can be generated to measure the uncertainty of prediction. This is applied to separating subjects with Alzheimer's disease from normal controls using a linear support vector machine on a region of interest in magnetic resonance images of the brain. We show that our proposed method leads to an improvement in discrimination using voxel-based morphometry and deformation tensor-based morphometry over bootstrap aggregating, a common ensemble learning framework. The proposed approach also generates more reasonable soft-classification predictions than bootstrap aggregating. We expect that this approach could be applied to other statistical prediction tasks where registration is important. PMID:23288332

  7. Smartphone app speeds registration.

    PubMed

    2011-03-01

    Two Denver area EDs have entered the digital world with the use of a mobile application that allows patients to pre-register before coming to the ED. Patients can use their smart phones to determine if they need to go to the ED and which one is closest. The ED registration desk receives the pre-registration form, which provides basic information, via fax. Once the information is received, registration notifies the charge nurse so the ED can prepare to receive the patient. PMID:21449510

  8. MO-C-17A-03: A GPU-Based Method for Validating Deformable Image Registration in Head and Neck Radiotherapy Using Biomechanical Modeling

    SciTech Connect

    Neylon, J; Min, Y; Qi, S; Kupelian, P; Santhanam, A

    2014-06-15

    Purpose: Deformable image registration (DIR) plays a pivotal role in head and neck adaptive radiotherapy but a systematic validation of DIR algorithms has been limited by a lack of quantitative high-resolution groundtruth. We address this limitation by developing a GPU-based framework that provides a systematic DIR validation by generating (a) model-guided synthetic CTs representing posture and physiological changes, and (b) model-guided landmark-based validation. Method: The GPU-based framework was developed to generate massive mass-spring biomechanical models from patient simulation CTs and contoured structures. The biomechanical model represented soft tissue deformations for known rigid skeletal motion. Posture changes were simulated by articulating skeletal anatomy, which subsequently applied elastic corrective forces upon the soft tissue. Physiological changes such as tumor regression and weight loss were simulated in a biomechanically precise manner. Synthetic CT data was then generated from the deformed anatomy. The initial and final positions for one hundred randomly-chosen mass elements inside each of the internal contoured structures were recorded as ground truth data. The process was automated to create 45 synthetic CT datasets for a given patient CT. For instance, the head rotation was varied between +/− 4 degrees along each axis, and tumor volumes were systematically reduced up to 30%. Finally, the original CT and deformed synthetic CT were registered using an optical flow based DIR. Results: Each synthetic data creation took approximately 28 seconds of computation time. The number of landmarks per data set varied between two and three thousand. The validation method is able to perform sub-voxel analysis of the DIR, and report the results by structure, giving a much more in depth investigation of the error. Conclusions: We presented a GPU based high-resolution biomechanical head and neck model to validate DIR algorithms by generating CT equivalent 3D

  9. Analytic regularization for landmark-based image registration

    NASA Astrophysics Data System (ADS)

    Shusharina, Nadezhda; Sharp, Gregory

    2012-03-01

    Landmark-based registration using radial basis functions (RBF) is an efficient and mathematically transparent method for the registration of medical images. To ensure invertibility and diffeomorphism of the RBF-based vector field, various regularization schemes have been suggested. Here, we report a novel analytic method of RBF regularization and demonstrate its power for Gaussian RBF. Our analytic formula can be used to obtain a regularized vector field from the solution of a system of linear equations, exactly as in traditional RBF, and can be generalized to any RBF with infinite support. We statistically validate the method on global registration of synthetic and pulmonary images. Furthermore, we present several clinical examples of multistage intensity/landmark-based registrations, where regularized Gaussian RBF are successful in correcting locally misregistered areas resulting from automatic B-spline registration. The intended ultimate application of our method is rapid, interactive local correction of deformable registration with a small number of mouse clicks.

  10. Biomechanical model as a registration tool for image-guided neurosurgery: evaluation against BSpline registration

    PubMed Central

    Mostayed, Ahmed; Garlapati, Revanth Reddy; Joldes, Grand Roman; Wittek, Adam; Roy, Aditi; Kikinis, Ron; Warfield, Simon K.; Miller, Karol

    2013-01-01

    In this paper we evaluate the accuracy of warping of neuro-images using brain deformation predicted by means of a patient-specific biomechanical model against registration using a BSpline-based free form deformation algorithm. Unlike the Bspline algorithm, biomechanics-based registration does not require an intra-operative MR image which is very expensive and cumbersome to acquire. Only sparse intra-operative data on the brain surface is sufficient to compute deformation for the whole brain. In this contribution the deformation fields obtained from both methods are qualitatively compared and overlaps of Canny edges extracted from the images are examined. We define an edge based Hausdorff distance metric to quantitatively evaluate the accuracy of registration for these two algorithms. The qualitative and quantitative evaluations indicate that our biomechanics-based registration algorithm, despite using much less input data, has at least as high registration accuracy as that of the BSpline algorithm. PMID:23771299

  11. Estimation of line-based target registration error

    NASA Astrophysics Data System (ADS)

    Ma, Burton; Peters, Terry M.; Chen, Elvis C. S.

    2016-03-01

    We present a novel method for estimating target registration error (TRE) in point-to-line registration. We develop a spatial stiffness model of the registration problem and derive the stiffness matrix of the model which leads to an analytic expression for predicting the root-mean-square (RMS) TRE. Under the assumption of isotropic localization noise, we show that the stiffness matrix for line-based registration is equal to the difference of the stiffness matrices for fiducial registration and surface-based registration. The expression for TRE is validated in the context of freehand ultrasound calibration performed using a tracked line fiducial as a calibration phantom. Measurements taken during calibration of a tracked linear ultrasound probe were used in simulations to assess TRE of point-to-line registration and the results were compared to the values predicted by the analytic expression. The difference between predicted and simulated RMS TRE magnitude for targets near the centroid of the registration points was less than 5% of the simulated magnitude when using more than 6 registration points. The difference between predicted and simulated RMS TRE magnitude for targets over the entire ultrasound image was almost always less than 10% of the simulated magnitude when using more than 10 registration points. TRE magnitude was minimized near the centroid of the registration points and the isocontours of TRE were elliptic in shape.

  12. A novel scheme for automatic nonrigid image registration using deformation invariant feature and geometric constraint

    NASA Astrophysics Data System (ADS)

    Deng, Zhipeng; Lei, Lin; Zhou, Shilin

    2015-10-01

    Automatic image registration is a vital yet challenging task, particularly for non-rigid deformation images which are more complicated and common in remote sensing images, such as distorted UAV (unmanned aerial vehicle) images or scanning imaging images caused by flutter. Traditional non-rigid image registration methods are based on the correctly matched corresponding landmarks, which usually needs artificial markers. It is a rather challenging task to locate the accurate position of the points and get accurate homonymy point sets. In this paper, we proposed an automatic non-rigid image registration algorithm which mainly consists of three steps: To begin with, we introduce an automatic feature point extraction method based on non-linear scale space and uniform distribution strategy to extract the points which are uniform distributed along the edge of the image. Next, we propose a hybrid point matching algorithm using DaLI (Deformation and Light Invariant) descriptor and local affine invariant geometric constraint based on triangulation which is constructed by K-nearest neighbor algorithm. Based on the accurate homonymy point sets, the two images are registrated by the model of TPS (Thin Plate Spline). Our method is demonstrated by three deliberately designed experiments. The first two experiments are designed to evaluate the distribution of point set and the correctly matching rate on synthetic data and real data respectively. The last experiment is designed on the non-rigid deformation remote sensing images and the three experimental results demonstrate the accuracy, robustness, and efficiency of the proposed algorithm compared with other traditional methods.

  13. 21 CFR 710.8 - Misbranding by reference to registration or to registration number.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... HUMAN SERVICES (CONTINUED) COSMETICS VOLUNTARY REGISTRATION OF COSMETIC PRODUCT ESTABLISHMENTS § 710.8 Misbranding by reference to registration or to registration number. Registration of a cosmetic...

  14. 21 CFR 710.8 - Misbranding by reference to registration or to registration number.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... HUMAN SERVICES (CONTINUED) COSMETICS VOLUNTARY REGISTRATION OF COSMETIC PRODUCT ESTABLISHMENTS § 710.8 Misbranding by reference to registration or to registration number. Registration of a cosmetic...

  15. 21 CFR 710.8 - Misbranding by reference to registration or to registration number.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... HUMAN SERVICES (CONTINUED) COSMETICS VOLUNTARY REGISTRATION OF COSMETIC PRODUCT ESTABLISHMENTS § 710.8 Misbranding by reference to registration or to registration number. Registration of a cosmetic...

  16. 21 CFR 710.8 - Misbranding by reference to registration or to registration number.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... HUMAN SERVICES (CONTINUED) COSMETICS VOLUNTARY REGISTRATION OF COSMETIC PRODUCT ESTABLISHMENTS § 710.8 Misbranding by reference to registration or to registration number. Registration of a cosmetic...

  17. 21 CFR 710.8 - Misbranding by reference to registration or to registration number.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... HUMAN SERVICES (CONTINUED) COSMETICS VOLUNTARY REGISTRATION OF COSMETIC PRODUCT ESTABLISHMENTS § 710.8 Misbranding by reference to registration or to registration number. Registration of a cosmetic...

  18. Development of simple and rapid elution methods for proteins from various affinity beads for their direct MALDI-TOF downstream application.

    PubMed

    Mlynarcik, Patrik; Bencurova, Elena; Madar, Marian; Mucha, Rastislav; Pulzova, Lucia; Hresko, Stanislav; Bhide, Mangesh

    2012-07-19

    Commercially available desalting techniques, necessary for downstream MALDI-TOF analysis of proteins, are often costly or time consuming for large-scale analysis. Here, we present techniques to elute proteins from various affinity resins, free from salt and ready for MALDI mass spectrometry. We showed that 0.1% TFA in 50% acetonitrile or 40% ethanol can be used as salt-free eluents for His-tagged proteins from variety of polyhistidine-affinity resins, while washing of resin beads twice with double-distilled water prior to the elution effectively desalted and recovered wide-range-molecular size proteins than commercially available desalting devices. Modified desalting and elution techniques were also applied for Flag- and Myc-tag affinity resins. The technique was further applied in co-precipitation assay, where the maximum recovery of wide-range molecular size proteins is crucial. Further, results showed that simple washing of the beads with double distilled water followed by elution with acetonitrile effectively desalted and recovered 150 kDa factor H protein of the sheep and its binding partner ~30 kDa BbCRASP-1 in co-precipitation assay. In summary, simple modifications in the desalting and elution strategy save time, labor and cost of the protein preparation for MALDI mass spectrometry; and large-scale protein purifications or co-precipitations can be performed with ease. PMID:22433248

  19. A new affinity method for purification of bovine testicular hyaluronidase enzyme and an investigation of the effects of some compounds on this enzyme.

    PubMed

    Kaya, Mustafa Oguzhan; Arslan, Oktay; Guler, Ozen Ozensoy

    2015-01-01

    In this study, a new affinity gel for the purification of bovine testicular hyaluronidase (BTH) was synthesized. L-Tyrosine was added as the extension arm to the Sepharose-4B activated with cyanogen bromide. m-Anisidine is a specific inhibitor of BTH enzyme. m-Anisidine was clamped to the newly formed Sepharose-4B-L-tyrosine as a ligand. As a result, an affinity gel having the chemical structure of Sepharose-4B-L-tyrosine-m-anisidine was obtained. BTH purified by ammonium sulfate precipitation and affinity chromatography was obtained with a 16.95% yield and 881.78 degree of purity. The kinetic constants K(M) and V(Max) for BTH were determined by using hyaluronic acid as a substrate. K(M) and V(Max) values obtained from the Lineweaver-Burk graph were found to be 2.23 mM and 19.85 U/mL, respectively. In vitro effects of some chemicals were determined on purified BTH enzyme. Some chemically active ingredients were 1,1-dimethyl piperidinium chloride, β-naphthoxyacetic acid and gibberellic acid. Gibberellic acid showed the best inhibition effect on BTH. PMID:25373501

  20. A simple enzyme-substrate localized conjugation method to generate immobilized, functional glutathione S-transferase fusion protein columns for affinity enrichment.

    PubMed

    Coughlin, John; Masci, Allyson; Gronke, Robert S; Bergelson, Svetlana; Co, Carl

    2016-07-15

    Immobilized protein receptors and enzymes are tools for isolating or enriching ligands and substrates based on affinity. For example, glutathione S-transferase (GST) is fused to proteins as a tag for binding to its substrate glutathione (GSH) linked to solid supports. One issue with this approach is that high-affinity interactions between receptors and ligands require harsh elution conditions such as low pH, which can result in leached receptor. Another issue is the inherent nonspecific chemical conjugation of reactive groups such as N-hydroxysuccinimide (NHS) that couple lysines to solid supports; the nonspecificity of NHS may result in residue modifications near the binding site(s) of the receptor that can affect ligand specificity. In this study, a simple conjugation procedure is presented that overcomes these limitations and results in immobilized GST fusion proteins that are functional and specific. Here, the affinity of GST for GSH was used to generate an enzyme-substrate site-specific cross-linking reaction; GSH-Sepharose was preactivated with 1-ethyl-3-(dimethylaminopropyl)carbodiimide (EDC) and then incubated Fc gamma receptor IIIa (FcγRIIIa)-GST. The immobilized FcγRIIIa-GST more specifically bound glycosylated immunoglobulin G1s (IgG1s) and was used to enrich nonfucosylated IgG1s from weaker binding species. This technique can be used when modifications of amino acids lead to changes in activity. PMID:27063248

  1. SULFUR PESTICIDE REGISTRATION STANDARD

    EPA Science Inventory

    The document contains information regarding reregistration of pesticide products containing the subject active ingredient. The document includes how to register under a registration standard, regulatory position and rationale, and summaries of data requirements and data gaps. Als...

  2. Vision-based registration for augmented reality system using monocular and binocular vision

    NASA Astrophysics Data System (ADS)

    Vallerand, Steve; Kanbara, Masayuki; Yokoya, Naokazu

    2003-05-01

    In vision-based augmented reality systems, the relation between the real and virtual worlds needs to be estimated to perform the registration of virtual objects. This paper suggests a vision-based registration method for video see-through augmented reality systems using binocular cameras which increases the quality of the registration performed using three points of a known marker. The originality of this work is the use of both monocular vision-based and stereoscopic vision-based techniques in order to complete the registration. Also, a method that performs a correction of the 2D positions in the images of the marker points is proposed. The correction improves the registration stability and accuracy of the system. The stability of the registration obtained with the proposed registration method combined or not with the correction method is compared to the registration obtained with standard stereoscopic registration.

  3. Registration of challenging pre-clinical brain images

    PubMed Central

    Crum, William R.; Modo, Michel; Vernon, Anthony C.; Barker, Gareth J.; Williams, Steven C.R.

    2013-01-01

    The size and complexity of brain imaging studies in pre-clinical populations are increasing, and automated image analysis pipelines are urgently required. Pre-clinical populations can be subjected to controlled interventions (e.g., targeted lesions), which significantly change the appearance of the brain obtained by imaging. Existing systems for registration (the systematic alignment of scans into a consistent anatomical coordinate system), which assume image similarity to a reference scan, may fail when applied to these images. However, affine registration is a particularly vital pre-processing step for subsequent image analysis which is assumed to be an effective procedure in recent literature describing sophisticated techniques such as manifold learning. Therefore, in this paper, we present an affine registration solution that uses a graphical model of a population to decompose difficult pairwise registrations into a composition of steps using other members of the population. We developed this methodology in the context of a pre-clinical model of stroke in which large, variable hyper-intense lesions significantly impact registration performance. We tested this technique systematically in a simulated human population of brain tumour images before applying it to pre-clinical models of Parkinson's disease and stroke. PMID:23558335

  4. Intensity-Based Registration for Lung Motion Estimation

    NASA Astrophysics Data System (ADS)

    Cao, Kunlin; Ding, Kai; Amelon, Ryan E.; Du, Kaifang; Reinhardt, Joseph M.; Raghavan, Madhavan L.; Christensen, Gary E.

    Image registration plays an important role within pulmonary image analysis. The task of registration is to find the spatial mapping that brings two images into alignment. Registration algorithms designed for matching 4D lung scans or two 3D scans acquired at different inflation levels can catch the temporal changes in position and shape of the region of interest. Accurate registration is critical to post-analysis of lung mechanics and motion estimation. In this chapter, we discuss lung-specific adaptations of intensity-based registration methods for 3D/4D lung images and review approaches for assessing registration accuracy. Then we introduce methods for estimating tissue motion and studying lung mechanics. Finally, we discuss methods for assessing and quantifying specific volume change, specific ventilation, strain/ stretch information and lobar sliding.

  5. MO-C-17A-02: A Novel Method for Evaluating Hepatic Stiffness Based On 4D-MRI and Deformable Image Registration

    SciTech Connect

    Cui, T; Liang, X; Czito, B; Palta, M; Bashir, M; Yin, F; Cai, J

    2014-06-15

    Purpose: Quantitative imaging of hepatic stiffness has significant potential in radiation therapy, ranging from treatment planning to response assessment. This study aims to develop a novel, noninvasive method to quantify liver stiffness with 3D strains liver maps using 4D-MRI and deformable image registration (DIR). Methods: Five patients with liver cancer were imaged with an institutionally developed 4D-MRI technique under an IRB-approved protocol. Displacement vector fields (DVFs) across the liver were generated via DIR of different phases of 4D-MRI. Strain tensor at each voxel of interest (VOI) was computed from the relative displacements between the VOI and each of the six adjacent voxels. Three principal strains (E{sub 1}, E{sub 2} and E{sub 3}) of the VOI were derived as the eigenvalue of the strain tensor, which represent the magnitudes of the maximum and minimum stretches. Strain tensors for two regions of interest (ROIs) were calculated and compared for each patient, one within the tumor (ROI{sub 1}) and the other in normal liver distant from the heart (ROI{sub 2}). Results: 3D strain maps were successfully generated fort each respiratory phase of 4D-MRI for all patients. Liver deformations induced by both respiration and cardiac motion were observed. Differences in strain values adjacent to the distant from the heart indicate significant deformation caused by cardiac expansion during diastole. The large E{sub 1}/E{sub 2} (∼2) and E{sub 1}/E{sub 2} (∼10) ratios reflect the predominance of liver deformation in the superior-inferior direction. The mean E{sub 1} in ROI{sub 1} (0.12±0.10) was smaller than in ROI{sub 2} (0.15±0.12), reflecting a higher degree of stiffness of the cirrhotic tumor. Conclusion: We have successfully developed a novel method for quantitatively evaluating regional hepatic stiffness based on DIR of 4D-MRI. Our initial findings indicate that liver strain is heterogeneous, and liver tumors may have lower principal strain values

  6. Real-time automatic registration in optical surgical navigation

    NASA Astrophysics Data System (ADS)

    Lin, Qinyong; Yang, Rongqian; Cai, Ken; Si, Xuan; Chen, Xiuwen; Wu, Xiaoming

    2016-05-01

    An image-guided surgical navigation system requires the improvement of the patient-to-image registration time to enhance the convenience of the registration procedure. A critical step in achieving this aim is performing a fully automatic patient-to-image registration. This study reports on a design of custom fiducial markers and the performance of a real-time automatic patient-to-image registration method using these markers on the basis of an optical tracking system for rigid anatomy. The custom fiducial markers are designed to be automatically localized in both patient and image spaces. An automatic localization method is performed by registering a point cloud sampled from the three dimensional (3D) pedestal model surface of a fiducial marker to each pedestal of fiducial markers searched in image space. A head phantom is constructed to estimate the performance of the real-time automatic registration method under four fiducial configurations. The head phantom experimental results demonstrate that the real-time automatic registration method is more convenient, rapid, and accurate than the manual method. The time required for each registration is approximately 0.1 s. The automatic localization method precisely localizes the fiducial markers in image space. The averaged target registration error for the four configurations is approximately 0.7 mm. The automatic registration performance is independent of the positions relative to the tracking system and the movement of the patient during the operation.

  7. Measuring an antibody affinity distribution molecule by molecule

    SciTech Connect

    Bradbury, Andrew M; Werner, James H; Temirov, Jamshid

    2008-01-01

    Single molecule fluorescence mIcroscopy was used to observe the binding and unbinding of hapten decorated quantum dots with individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.

  8. Affinity Peptide for Targeted Detection of Dysplasia in Barrett's Esophagus

    PubMed Central

    Li, Meng; Anastassiades, Costas P.; Joshi, Bishnu; Komarck, Chris M.; Piraka, Cyrus; Elmunzer, Badih J.; Turgeon, Danielle K.; Johnson, Timothy D.; Appelman, Henry; Beer, David G.; Wang, Thomas D.

    2012-01-01

    Background & Aims Dysplasia is a pre-malignant condition in Barrett's esophagus that is difficult to detect on screening endoscopy because of its flat architecture and patchy distribution. Peptides are promising for use as novel molecular probes that identify cell surface targets unique to disease, and can be fluorescence-labeled for detection. We aim to select and validate an affinity peptide that binds to esophageal dysplasia for future clinical studies. Methods Peptide selection was performed using phage display by removing non-specific binders using Q-hTERT (intestinal metaplasia) cells and achieving specific binding against OE33 (esophageal adenocarcinoma) cells. Selective binding was confirmed on bound phage counts, ELISA, flow cytometry, competitive inhibition, and fluorescence microscopy. On stereomicroscopy, specific peptide binding to dysplasia on endoscopically resected specimens was assessed by rigorous registration of fluorescence intensity to histology in 1 mm intervals. Results The peptide sequence SNFYMPL was selected and demonstrated preferential binding to target cells on bound phage counts, ELISA, and flow cytometry. Reducing binding was observed on competition with unlabeled peptide in a dose dependent manner, an affinity of Kd = 164 nM was measured, and peptide binding to the surface of OE33 cells was validated on fluorescence microscopy. On esophageal specimens (n=12), the fluorescence intensity (mean±SEM) in 1 mm intervals classified histologically as squamous (n=145), intestinal metaplasia (n=83), dysplasia (n=61) and gastric mucosa (n=69) was 46.5±1.6, 62.3±5.8, 100.0±9.0, and 42.4±3.0 arb units, respectively. Conclusions The peptide sequence SNFYMPL binds specifically to dysplasia in Barrett's esophagus, and can be fluorescence-labeled to target pre-malignant mucosa on imaging. PMID:20637198

  9. 14 CFR 47.15 - Registration number.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 1 2011-01-01 2011-01-01 false Registration number. 47.15 Section 47.15... REGISTRATION General § 47.15 Registration number. (a) Number required. An applicant for aircraft registration must place a U.S. registration number (registration mark) on the Aircraft Registration Application,...

  10. 14 CFR 47.15 - Registration number.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 1 2012-01-01 2012-01-01 false Registration number. 47.15 Section 47.15... REGISTRATION General § 47.15 Registration number. (a) Number required. An applicant for aircraft registration must place a U.S. registration number (registration mark) on the Aircraft Registration Application,...

  11. 14 CFR 47.15 - Registration number.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 1 2013-01-01 2013-01-01 false Registration number. 47.15 Section 47.15... REGISTRATION General § 47.15 Registration number. (a) Number required. An applicant for aircraft registration must place a U.S. registration number (registration mark) on the Aircraft Registration Application,...

  12. Point-to-Volume Registration of Prostate Implants to Ultrasound★

    PubMed Central

    Dehghan, Ehsan; Lee, Junghoon; Fallavollita, Pascal; Kuo, Nathanael; Deguet, Anton; Burdette, E. Clif; Song, Danny; Prince, Jerry L.; Fichtinger, Gabor

    2011-01-01

    Ultrasound-Fluoroscopy fusion is a key step toward intra-operative dosimetry for prostate brachytherapy. We propose a method for intensity-based registration of fluoroscopy to ultrasound that obviates the need for seed segmentation required for seed-based registration. We employ image thresholding and morphological and Gaussian filtering to enhance the image intensity distribution of ultrasound volume. Finally, we find the registration parameters by maximizing a point-to-volume similarity metric. We conducted an experiment on a ground truth phantom and achieved registration error of 0.7±0.2 mm. Our clinical results on 5 patient data sets show excellent visual agreement between the registered seeds and the ultrasound volume with a seed-to-seed registration error of 1.8±0.9 mm. With low registration error, high computational speed and no need for manual seed segmentation, our method is promising for clinical application. PMID:21995080

  13. Longitudinal brain MRI analysis with uncertain registration.

    PubMed

    Simpson, Ivor J A; Woolrich, Mark W; Groves, Adrian R; Schnabel, Julia A

    2011-01-01

    In this paper we propose a novel approach for incorporating measures of spatial uncertainty, which are derived from non-rigid registration, into spatially normalised statistics. Current approaches to spatially normalised statistical analysis use point-estimates of the registration parameters. This is limiting as the registration will rarely be completely accurate, and therefore data smoothing is often used to compensate for the uncertainty of the mapping. We derive localised measurements of spatial uncertainty from a probabilistic registration framework, which provides a principled approach to image smoothing. We evaluate our method using longitudinal deformation features from a set of MR brain images acquired from the Alzheimer's Disease Neuroimaging Initiative. These images are spatially normalised using our probabilistic registration algorithm. The spatially normalised longitudinal features are adaptively smoothed according to the registration uncertainty. The proposed adaptive smoothing shows improved classification results, (84% correct Alzheimer's Disease vs. controls), over either not smoothing (79.6%), or using a Gaussian filter with sigma = 2mm (78.8%). PMID:21995084

  14. Registration of point cloud data for HDD stamped base inspection

    NASA Astrophysics Data System (ADS)

    Suh, Sungho; Cho, Hansang

    2015-09-01

    As a part of the HDD manufacturing process, HDD stamped base, an exterior container, is one of the most essential components in which various parts become assembled to compose a hard disk drive (HDD). Height errors that are caused by pressing, breaking or cracking can occur on the base, because it is designed by a stamping method. In order to detect the height errors, the inspection process is essential in the production fields. In the current industry, CMM (Coordinate Measurement Machine) is one of the representative machines that inspect certain regions on the product. The machine probes a designated point by an operator and judges the defect by comparing the height of the point to the originally designed height. However, the method takes much time to inspect each designated point resulting in a total of 17 minutes. In order to reduce the total inspection time, we propose an inspection method using 3D point cloud data acquired from a holographic sensor. To compare the height from acquired 3D point cloud data with the one from the originally designed CAD data, the exact point cloud registration is important. There are differences between 2D image registration and 3D point cloud registration, such as translation on each plane, rotation, tilt, and nonlinear transformations. The relationship between the acquired 3D point cloud data and the originally designed CAD data can be obtained by projective transformation. If the projective transformation matrix between the two is obtained, 3D point cloud data registration can be performed. In order to calculate 3D projective transformation matrix, corresponding points between 3D point cloud data and CAD data are required. To find the corresponding points, we use the height map which is projected from 3D point cloud data onto XY plane. The height map has pixel intensity from the height value of each point. If the height maps from 3D point cloud data and CAD data are matched, corresponding points can be estimated. As one of the

  15. Robust Deformable Image Registration using Prior Shape Information for Atlas to Patient Registration

    PubMed Central

    Ellingsen, Lotta M.; Chintalapani, Gouthami; Taylor, Russell H.; Prince, Jerry L.

    2009-01-01

    Statistical atlases enable the individualization of atlas information for patient specific applications such as surgical planning. In this paper, a statistical atlas comprising a point distribution model defined on the vertices of a tetrahedral mesh is registered to a subject’s computed tomography scan of the human pelvis. The approach consists of a volumetric deformable registration method augmented to maintain the topology of the atlas mesh after deformation as well as incorporating the dominant three-dimensional shape modes in the atlas. Experimental results demonstrate that incorporation of the statistical shape atlas helps to stabilize the registration and improves robustness and registration accuracy. PMID:19515532

  16. User Registration in EOSDIS

    NASA Astrophysics Data System (ADS)

    Murphy, K. J.; Mitchell, A. E.

    2009-12-01

    Throughout the lifetime of EOSDIS the topic of user registration has received varied attention. Initially, for example, users ordering data from the Earth Science Data Gateway were required to register for delivery of media orders, to check order status and save profile information for future interactions. As EOSDIS embraced evolution of its data systems, the mostly centralized search and order system was replaced with a more diverse set of interfaces allowing (mostly) anonymous online access to data, tools and services. The changes to EOSDIS were embraced by users but the anonymous nature of the interaction made it more difficult to characterize users, capture metrics and provide customized services that benefit users. Additionally, new tools and interfaces have been developed without a centralized registration system. Currently a patchwork of independent registration systems exists throughout EOSDIS for ordering data and interacting with online tools and services. Each requires a separate username and password that must be managed by users. A consolidation of registration systems presents an opportunity to improve not only the user experience through tool customization and simplification of password management, but the understanding of users. This work discusses the options for implementing a common user registration for the EOSDIS, anticipated benefits and pitfalls.

  17. Aptamer Affinity Maturation by Resampling and Microarray Selection.

    PubMed

    Kinghorn, Andrew B; Dirkzwager, Roderick M; Liang, Shaolin; Cheung, Yee-Wai; Fraser, Lewis A; Shiu, Simon Chi-Chin; Tang, Marco S L; Tanner, Julian A

    2016-07-19

    Aptamers have significant potential as affinity reagents, but better approaches are critically needed to discover higher affinity nucleic acids to widen the scope for their diagnostic, therapeutic, and proteomic application. Here, we report aptamer affinity maturation, a novel aptamer enhancement technique, which combines bioinformatic resampling of aptamer sequence data and microarray selection to navigate the combinatorial chemistry binding landscape. Aptamer affinity maturation is shown to improve aptamer affinity by an order of magnitude in a single round. The novel aptamers exhibited significant adaptation, the complexity of which precludes discovery by other microarray based methods. Honing aptamer sequences using aptamer affinity maturation could help optimize a next generation of nucleic acid affinity reagents. PMID:27346322

  18. Immobilized metal ion affinity chromatography.

    PubMed

    Yip, T T; Hutchens, T W

    1992-01-01

    Immobilized metal ion affinity chromatography (IMAC) (1,2) is also referred to as metal chelate chromatography, metal ion interaction chromatography, and ligand-exchange chromatography. We view this affinity separation technique as an intermediate between highly specific, high-affinity bioaffinity separation methods, and wider spectrum, low-specificity adsorption methods, such as ion exchange. The IMAC stationary phases are designed to chelate certain metal ions that have selectivity for specific groups (e.g., His residues) in peptides (e.g., 3-7) and on protein surfaces (8-13). The number of stationary phases that can be synthesized for efficient chelation of metal ions is unlimited, but the critical consideration is that there must be enough exposure of the metal ion to interact with the proteins, preferably in a biospecific manner. Several examples are presented in Fig. 1. The challenge to produce new immobilized chelating groups, including protein surface metal-binding domains (14,15) is being explored continuously. Table 1 presents a list of published procedures for the synthesis and use of stationary phases with immobilized chelating groups. This is by no means exhaustive, and is intended only to give an idea of the scope and versatility of IMAC. Fig. 1 Schematic illustration of several types of immobilized metal-chelating groups, including, iminodiacetate (IDA), tris(carboxymethyl) ethylenediamine (TED), and the metal-binding peptides (GHHPH)(n)G (where n = 1,2,3, and 5) (14,15). Table 1 Immobilized Chelating Groups and Metal Ions Used for Immobilized Metal Ion Affinity Chromatography Chelating group Suitable metal ions Reference Commercial source Immodiacetate Transitional1,2 Pharmacia LKB Pierce Sigma Boehringer Mannheim TosoHaas 2-Hydroxy-3[N-(2- pyrtdylmethyl) glycme]propyl Transitional3 Not available ?-Alky1 mtrilo triacetic acid Transitional4 Not available Carboxymethylated asparhc acid Ca(II)13 Not available Tris (carboxy- methyl) ethylene Diamme

  19. Mass preserving registration for lung CT

    NASA Astrophysics Data System (ADS)

    Gorbunova, Vladlena; Lo, Pechin; Loeve, Martine; Tiddens, Harm A.; Sporring, Jon; Nielsen, Mads; de Bruijne, Marleen

    2009-02-01

    In this paper, we evaluate a novel image registration method on a set of expiratory-inspiratory pairs of computed tomography (CT) lung scans. A free-form multi resolution image registration technique is used to match two scans of the same subject. To account for the differences in the lung intensities due to differences in inspiration level, we propose to adjust the intensity of lung tissue according to the local expansion or compression. An image registration method without intensity adjustment is compared to the proposed method. Both approaches are evaluated on a set of 10 pairs of expiration and inspiration CT scans of children with cystic fibrosis lung disease. The proposed method with mass preserving adjustment results in significantly better alignment of the vessel trees. Analysis of local volume change for regions with trapped air compared to normally ventilated regions revealed larger differences between these regions in the case of mass preserving image registration, indicating that mass preserving registration is better at capturing localized differences in lung deformation.

  20. 3D–2D registration for surgical guidance: effect of projection view angles on registration accuracy

    PubMed Central

    Uneri, A; Otake, Y; Wang, A S; Kleinszig, G; Vogt, S; Khanna, A J; Siewerdsen, J H

    2016-01-01

    An algorithm for intensity-based 3D–2D registration of CT and x-ray projections is evaluated, specifically using single- or dual-projection views to provide 3D localization. The registration framework employs the gradient information similarity metric and covariance matrix adaptation evolution strategy to solve for the patient pose in six degrees of freedom. Registration performance was evaluated in an anthropomorphic phantom and cadaver, using C-arm projection views acquired at angular separation, Δθ, ranging from ~0°–180° at variable C-arm magnification. Registration accuracy was assessed in terms of 2D projection distance error and 3D target registration error (TRE) and compared to that of an electromagnetic (EM) tracker. The results indicate that angular separation as small as Δθ ~10°–20° achieved TRE <2 mm with 95% confidence, comparable or superior to that of the EM tracker. The method allows direct registration of preoperative CT and planning data to intraoperative fluoroscopy, providing 3D localization free from conventional limitations associated with external fiducial markers, stereotactic frames, trackers and manual registration. PMID:24351769

  1. 3D-2D registration for surgical guidance: effect of projection view angles on registration accuracy

    NASA Astrophysics Data System (ADS)

    Uneri, A.; Otake, Y.; Wang, A. S.; Kleinszig, G.; Vogt, S.; Khanna, A. J.; Siewerdsen, J. H.

    2014-01-01

    An algorithm for intensity-based 3D-2D registration of CT and x-ray projections is evaluated, specifically using single- or dual-projection views to provide 3D localization. The registration framework employs the gradient information similarity metric and covariance matrix adaptation evolution strategy to solve for the patient pose in six degrees of freedom. Registration performance was evaluated in an anthropomorphic phantom and cadaver, using C-arm projection views acquired at angular separation, Δθ, ranging from ˜0°-180° at variable C-arm magnification. Registration accuracy was assessed in terms of 2D projection distance error and 3D target registration error (TRE) and compared to that of an electromagnetic (EM) tracker. The results indicate that angular separation as small as Δθ ˜10°-20° achieved TRE <2 mm with 95% confidence, comparable or superior to that of the EM tracker. The method allows direct registration of preoperative CT and planning data to intraoperative fluoroscopy, providing 3D localization free from conventional limitations associated with external fiducial markers, stereotactic frames, trackers and manual registration.

  2. Surface-based prostate registration with biomechanical regularization

    NASA Astrophysics Data System (ADS)

    van de Ven, Wendy J. M.; Hu, Yipeng; Barentsz, Jelle O.; Karssemeijer, Nico; Barratt, Dean; Huisman, Henkjan J.

    2013-03-01

    Adding MR-derived information to standard transrectal ultrasound (TRUS) images for guiding prostate biopsy is of substantial clinical interest. A tumor visible on MR images can be projected on ultrasound by using MRUS registration. A common approach is to use surface-based registration. We hypothesize that biomechanical modeling will better control deformation inside the prostate than a regular surface-based registration method. We developed a novel method by extending a surface-based registration with finite element (FE) simulation to better predict internal deformation of the prostate. For each of six patients, a tetrahedral mesh was constructed from the manual prostate segmentation. Next, the internal prostate deformation was simulated using the derived radial surface displacement as boundary condition. The deformation field within the gland was calculated using the predicted FE node displacements and thin-plate spline interpolation. We tested our method on MR guided MR biopsy imaging data, as landmarks can easily be identified on MR images. For evaluation of the registration accuracy we used 45 anatomical landmarks located in all regions of the prostate. Our results show that the median target registration error of a surface-based registration with biomechanical regularization is 1.88 mm, which is significantly different from 2.61 mm without biomechanical regularization. We can conclude that biomechanical FE modeling has the potential to improve the accuracy of multimodal prostate registration when comparing it to regular surface-based registration.

  3. Image registration by parts

    NASA Technical Reports Server (NTRS)

    Chalermwat, Prachya; El-Ghazawi, Tarek; LeMoigne, Jacqueline

    1997-01-01

    In spite of the large number of different image registration techniques, most of these techniques use the correlation operation to match spatial image characteristics. Correlation is known to be one of the most computationally intensive operations and its computational needs grow rapidly with the increase in the image sizes. In this article, we show that, in many cases, it might be sufficient to determine image transformations by considering only one or several parts of the image rather than the entire image, which could result in substantial computational savings. This paper introduces the concept of registration by parts and investigates its viability. It describes alternative techniques for such image registration by parts and presents early empirical results that address the underlying trade-offs.

  4. Towards operational multisensor registration

    NASA Technical Reports Server (NTRS)

    Rignot, Eric J. M.; Kwok, Ronald; Curlander, John C.

    1991-01-01

    To use data from a number of different remote sensors in a synergistic manner, a multidimensional analysis of the data is necessary. However, prior to this analysis, processing to correct for the systematic geometric distortion characteristic of each sensor is required. Furthermore, the registration process must be fully automated to handle a large volume of data and high data rates. A conceptual approach towards an operational multisensor registration algorithm is presented. The performance requirements of the algorithm are first formulated given the spatially, temporally, and spectrally varying factors that influence the image characteristics and the science requirements of various applications. Several registration techniques that fit within the structure of this algorithm are also presented. Their performance was evaluated using a multisensor test data set assembled from LANDSAT TM, SEASAT, SIR-B, Thermal Infrared Multispectral Scanner (TIMS), and SPOT sensors.

  5. Local Affinity Release.

    PubMed

    Delplace, Vianney; Obermeyer, Jaclyn; Shoichet, Molly S

    2016-07-26

    The use of hydrogels for therapeutic delivery is a burgeoning area of investigation. These water-swollen polymer matrices are ideal platforms for localized drug delivery that can be further combined with specific ligands or nanotechnologies to advance the controlled release of small-molecule drugs and proteins. Due to the advantage of hydrophobic, electrostatic, or specific extracellular matrix interactions, affinity-based strategies can overcome burst release and challenges associated with encapsulation. Future studies will provide innovative binding tools, truly stimuli-responsive systems, and original combinations of emerging technologies to control the release of therapeutics spatially and temporally. Local drug delivery can be achieved by directly injecting a therapeutic to its site of action and is advantageous because off-target effects associated with systemic delivery can be minimized. For prolonged benefit, a vehicle that provides sustained drug release is required. Hydrogels are versatile platforms for localized drug release, owing to the large library of biocompatible building blocks from which they can be formed. Injectable hydrogel formulations that gel quickly in situ and provide sustained release of therapeutics are particularly advantageous to minimize invasiveness. The incorporation of polymers, ligands or nanoparticles that have an affinity for the therapeutic of interest improve control over the release of small-molecule drugs and proteins from hydrogels, enabling spatial and temporal control over the delivery. Such affinity-based strategies can overcome drug burst release and challenges associated with protein instability, allowing more effective therapeutic molecule delivery for a range of applications from therapeutic contact lenses to ischemic tissue regeneration. PMID:27403513

  6. Medical image registration using fuzzy theory.

    PubMed

    Pan, Meisen; Tang, Jingtian; Xiong, Qi

    2012-01-01

    Mutual information (MI)-based registration, which uses MI as the similarity measure, is a representative method in medical image registration. It has an excellent robustness and accuracy, but with the disadvantages of a large amount of calculation and a long processing time. In this paper, by computing the medical image moments, the centroid is acquired. By applying fuzzy c-means clustering, the coordinates of the medical image are divided into two clusters to fit a straight line, and the rotation angles of the reference and floating images are computed, respectively. Thereby, the initial values for registering the images are determined. When searching the optimal geometric transformation parameters, we put forward the two new concepts of fuzzy distance and fuzzy signal-to-noise ratio (FSNR), and we select FSNR as the similarity measure between the reference and floating images. In the experiments, the Simplex method is chosen as multi-parameter optimisation. The experimental results show that this proposed method has a simple implementation, a low computational cost, a fast registration and good registration accuracy. Moreover, it can effectively avoid trapping into the local optima. It is adapted to both mono-modality and multi-modality image registrations. PMID:21442490

  7. Lucas-Kanade image registration using camera parameters

    NASA Astrophysics Data System (ADS)

    Cho, Sunghyun; Cho, Hojin; Tai, Yu-Wing; Moon, Young Su; Cho, Junguk; Lee, Shihwa; Lee, Seungyong

    2012-01-01

    The Lucas-Kanade algorithm and its variants have been successfully used for numerous works in computer vision, which include image registration as a component in the process. In this paper, we propose a Lucas-Kanade based image registration method using camera parameters. We decompose a homography into camera intrinsic and extrinsic parameters, and assume that the intrinsic parameters are given, e.g., from the EXIF information of a photograph. We then estimate only the extrinsic parameters for image registration, considering two types of camera motions, 3D rotations and full 3D motions with translations and rotations. As the known information about the camera is fully utilized, the proposed method can perform image registration more reliably. In addition, as the number of extrinsic parameters is smaller than the number of homography elements, our method runs faster than the Lucas-Kanade based registration method that estimates a homography itself.

  8. Classification of neocortical interneurons using affinity propagation

    PubMed Central

    Santana, Roberto; McGarry, Laura M.; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits. PMID:24348339

  9. Classification of neocortical interneurons using affinity propagation.

    PubMed

    Santana, Roberto; McGarry, Laura M; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits. PMID:24348339

  10. Automatic sub-volume registration by probabilistic random search

    NASA Astrophysics Data System (ADS)

    Han, Jingfeng; Qiao, Min; Hornegger, Joachim; Kuwert, Torsten; Bautz, Werner; Römer, Wolfgang

    2006-03-01

    Registration of an individual's image data set to an anatomical atlas provides valuable information to the physician. In many cases, the individual image data sets are partial data, which may be mapped to one part or one organ of the entire atlas data. Most of the existing intensity based image registration approaches are designed to align images of the entire view. When they are applied to the registration with partial data, a manual pre-registration is usually required. This paper proposes a fully automatic approach to the registration of the incomplete image data to an anatomical atlas. The spatial transformations are modelled as any parametric functions. The proposed method is built upon a random search mechanism, which allows to find the optimal transformation randomly and globally even when the initialization is not ideal. It works more reliably than the existing methods for the partial data registration because it successfully overcomes the local optimum problem. With appropriate similarity measures, this framework is applicable to both mono-modal and multi-modal registration problems with partial data. The contribution of this work is the description of the mathematical framework of the proposed algorithm and the implementation of the related software. The medical evaluation on the MRI data and the comparison of the proposed method with different existing registration methods show the feasibility and superiority of the proposed method.

  11. Hierarchical estimation of a dense deformation field for 3-D robust registration.

    PubMed

    Hellier, P; Barillot, C; Mémin, E; Pérez, P

    2001-05-01

    A new method for medical image registration is formulated as a minimization problem involving robust estimators. We propose an efficient hierarchical optimization framework which is both multiresolution and multigrid. An anatomical segmentation of the cortex is introduced in the adaptive partitioning of the volume on which the multigrid minimization is based. This allows to limit the estimation to the areas of interest, to accelerate the algorithm, and to refine the estimation in specified areas. At each stage of the hierarchical estimation, we refine current estimate by seeking a piecewise affine model for the incremental deformation field. The performance of this method is numerically evaluated on simulated data and its benefits and robustness are shown on a database of 18 magnetic resonance imaging scans of the head. PMID:11403198

  12. Distributed Continuous Registration.

    ERIC Educational Resources Information Center

    Myers, Donald L.

    1981-01-01

    The development, implementation, and features of Northern Colorado's continuous registration system are described. The system is an online distributed processing system, written in COBOL for an IBM Series I under the CPS operating system. Course selection, permit to enroll, and drop/add forms are provided. (Author/MLW)

  13. CUNY's Voter Registration System.

    ERIC Educational Resources Information Center

    Hershenson, Jay; And Others

    This collection of items including public testimony by the Vice Chancellor, Jay Hershenson, a formal resolution, a press release, and brochures, documents the City University of New York's (CUNY) unique voter registration system, "CUNY Project Vote". As the press release describes it, Project Vote is the nation's largest student voter registration…

  14. Registration Study. Research Note.

    ERIC Educational Resources Information Center

    Baratta, Mary Kathryne

    During spring 1977 registration, 3,255 or 45% of Moraine Valley Community College (MVCC) registering students responded to a scheduling preferences and problems questionnaire covering enrollment status, curriculum load, program preference, ability to obtain courses, schedule conflicts, preferred times for class offerings, actual scheduling of…

  15. Nonrigid image registration using an entropic similarity.

    PubMed

    Khader, Mohammed; Ben Hamza, A

    2011-09-01

    In this paper, we propose a nonrigid image registration technique by optimizing a generalized information-theoretic similarity measure using the quasi-Newton method as an optimization scheme and cubic B-splines for modeling the nonrigid deformation field between the fixed and moving 3-D image pairs. To achieve a compromise between the nonrigid registration accuracy and the associated computational cost, we implement a three-level hierarchical multiresolution approach such that the image resolution is increased in a coarse to fine fashion. Experimental results are provided to demonstrate the registration accuracy of our approach. The feasibility of the proposed method is demonstrated on a 3-D magnetic resonance data volume and also on clinically acquired 4-D CT image datasets. PMID:21690017

  16. The hidden KPI registration accuracy.

    PubMed

    Shorrosh, Paul

    2011-09-01

    Determining the registration accuracy rate is fundamental to improving revenue cycle key performance indicators. A registration quality assurance (QA) process allows errors to be corrected before bills are sent and helps registrars learn from their mistakes. Tools are available to help patient access staff who perform registration QA manually. PMID:21923052

  17. Outline of Programe Registration System

    NASA Astrophysics Data System (ADS)

    Kono, Masamichi

    After the outline of the copyright registration system was described in this paper, the program registration system, which has started from April l, 1987, was introduced in focussing on the subjects as the special case and a methodology of registration procedures and how to submit the application.

  18. Multimodality imaging combination in small animal via point-based registration

    NASA Astrophysics Data System (ADS)

    Yang, C. C.; Wu, T. H.; Lin, M. H.; Huang, Y. H.; Guo, W. Y.; Chen, C. L.; Wang, T. C.; Yin, W. H.; Lee, J. S.

    2006-12-01

    We present a system of image co-registration in small animal study. Marker-based registration is chosen because of its considerable advantage that the fiducial feature is independent of imaging modality. We also experimented with different scanning protocols and different fiducial marker sizes to improve registration accuracy. Co-registration was conducted using rat phantom fixed by stereotactic frame. Overall, the co-registration accuracy was in sub-millimeter level and close to intrinsic system error. Therefore, we conclude that the system is an accurate co-registration method to be used in small animal studies.

  19. A complete software application for automatic registration of x-ray mammography and magnetic resonance images

    SciTech Connect

    Solves-Llorens, J. A.; Rupérez, M. J. Monserrat, C.; Lloret, M.

    2014-08-15

    Purpose: This work presents a complete and automatic software application to aid radiologists in breast cancer diagnosis. The application is a fully automated method that performs a complete registration of magnetic resonance (MR) images and x-ray (XR) images in both directions (from MR to XR and from XR to MR) and for both x-ray mammograms, craniocaudal (CC), and mediolateral oblique (MLO). This new approximation allows radiologists to mark points in the MR images and, without any manual intervention, it provides their corresponding points in both types of XR mammograms and vice versa. Methods: The application automatically segments magnetic resonance images and x-ray images using the C-Means method and the Otsu method, respectively. It compresses the magnetic resonance images in both directions, CC and MLO, using a biomechanical model of the breast that distinguishes the specific biomechanical behavior of each one of its three tissues (skin, fat, and glandular tissue) separately. It makes a projection of both compressions and registers them with the original XR images using affine transformations and nonrigid registration methods. Results: The application has been validated by two expert radiologists. This was carried out through a quantitative validation on 14 data sets in which the Euclidean distance between points marked by the radiologists and the corresponding points obtained by the application were measured. The results showed a mean error of 4.2 ± 1.9 mm for the MRI to CC registration, 4.8 ± 1.3 mm for the MRI to MLO registration, and 4.1 ± 1.3 mm for the CC and MLO to MRI registration. Conclusions: A complete software application that automatically registers XR and MR images of the breast has been implemented. The application permits radiologists to estimate the position of a lesion that is suspected of being a tumor in an imaging modality based on its position in another different modality with a clinically acceptable error. The results show that the

  20. 14 CFR 47.43 - Invalid registration.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Invalid registration. 47.43 Section 47.43... REGISTRATION Certificates of Aircraft Registration § 47.43 Invalid registration. (a) The registration of an...) compliance with 49 U.S.C. 44101-44104. (b) If the registration of an aircraft is invalid under paragraph...

  1. Image registration with auto-mapped control volumes

    SciTech Connect

    Schreibmann, Eduard; Xing Lei

    2006-04-15

    Many image registration algorithms rely on the use of homologous control points on the two input image sets to be registered. In reality, the interactive identification of the control points on both images is tedious, difficult, and often a source of error. We propose a two-step algorithm to automatically identify homologous regions that are used as a priori information during the image registration procedure. First, a number of small control volumes having distinct anatomical features are identified on the model image in a somewhat arbitrary fashion. Instead of attempting to find their correspondences in the reference image through user interaction, in the proposed method, each of the control regions is mapped to the corresponding part of the reference image by using an automated image registration algorithm. A normalized cross-correlation (NCC) function or mutual information was used as the auto-mapping metric and a limited memory Broyden-Fletcher-Goldfarb-Shanno algorithm (L-BFGS) was employed to optimize the function to find the optimal mapping. For rigid registration, the transformation parameters of the system are obtained by averaging that derived from the individual control volumes. In our deformable calculation, the mapped control volumes are treated as the nodes or control points with known positions on the two images. If the number of control volumes is not enough to cover the whole image to be registered, additional nodes are placed on the model image and then located on the reference image in a manner similar to the conventional BSpline deformable calculation. For deformable registration, the established correspondence by the auto-mapped control volumes provides valuable guidance for the registration calculation and greatly reduces the dimensionality of the problem. The performance of the two-step registrations was applied to three rigid registration cases (two PET-CT registrations and a brain MRI-CT registration) and one deformable registration of

  2. The Effect of Late Registration for College Classes

    ERIC Educational Resources Information Center

    Safer, Alan M.

    2009-01-01

    Objective: To assess the outcome of late registration for college classes and early class withdrawal. Method: Computerized 2007-9 school record data on 7,200 college students were analyzed to evaluate the effect of late class registration on the class grade--relative to the average class grade--and on class withdrawal. Assessed by multiple…

  3. 78 FR 20619 - Customer Account Registration and Maintenance

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-05

    ... United States Patent and Trademark Office Customer Account Registration and Maintenance ACTION: Proposed... methods: Email: InformationCollection@uspto.gov . Include ``0651- 00xx Customer Account Registration and... optional customer portal that will serve as a central point for access to online system interfaces...

  4. Temporal mammogram image registration using optimized curvilinear coordinates.

    PubMed

    Abdel-Nasser, Mohamed; Moreno, Antonio; Puig, Domenec

    2016-04-01

    Registration of mammograms plays an important role in breast cancer computer-aided diagnosis systems. Radiologists usually compare mammogram images in order to detect abnormalities. The comparison of mammograms requires a registration between them. A temporal mammogram registration method is proposed in this paper. It is based on the curvilinear coordinates, which are utilized to cope both with global and local deformations in the breast area. Temporal mammogram pairs are used to validate the proposed method. After registration, the similarity between the mammograms is maximized, and the distance between manually defined landmarks is decreased. In addition, a thorough comparison with the state-of-the-art mammogram registration methods is performed to show its effectiveness. PMID:27000285

  5. Adjoint affine fusion and tadpoles

    NASA Astrophysics Data System (ADS)

    Urichuk, Andrew; Walton, Mark A.

    2016-06-01

    We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are written for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.

  6. PROFESSIONAL REGISTRATION OF GOVERNMENT ENGINEERS.

    USGS Publications Warehouse

    Buchanan, Thomas J.

    1985-01-01

    The American Society of Civil Engineers views professional registration as an appropriate requirement for engineers, including those in government. The National Society of Professional Engineers makes registration a requirement for the grade of member and full privileges in the society. Some Federal agencies require engineering registration for certain positions in their agencies. Engineers in government service should consider the value of engineering registration to themselves and to their agencies and take pride in their professions and in their own capabilities by becoming registered engineers. They should also take steps to encourage their agencies to give more attention to engineering registration.

  7. Microscopic validation of whole mouse micro-metastatic tumor imaging agents using cryo-imaging and sliding organ image registration

    NASA Astrophysics Data System (ADS)

    Liu, Yiqiao; Zhou, Bo; Qutaish, Mohammed; Wilson, David L.

    2016-03-01

    We created a metastasis imaging, analysis platform consisting of software and multi-spectral cryo-imaging system suitable for evaluating emerging imaging agents targeting micro-metastatic tumor. We analyzed CREKA-Gd in MRI, followed by cryo-imaging which repeatedly sectioned and tiled microscope images of the tissue block face, providing anatomical bright field and molecular fluorescence, enabling 3D microscopic imaging of the entire mouse with single metastatic cell sensitivity. To register MRI volumes to the cryo bright field reference, we used our standard mutual information, non-rigid registration which proceeded: preprocess --> affine --> B-spline non-rigid 3D registration. In this report, we created two modified approaches: mask where we registered locally over a smaller rectangular solid, and sliding organ. Briefly, in sliding organ, we segmented the organ, registered the organ and body volumes separately and combined results. Though sliding organ required manual annotation, it provided the best result as a standard to measure other registration methods. Regularization parameters for standard and mask methods were optimized in a grid search. Evaluations consisted of DICE, and visual scoring of a checkerboard display. Standard had accuracy of 2 voxels in all regions except near the kidney, where there were 5 voxels sliding. After mask and sliding organ correction, kidneys sliding were within 2 voxels, and Dice overlap increased 4%-10% in mask compared to standard. Mask generated comparable results with sliding organ and allowed a semi-automatic process.

  8. Image registration using redundant wavelet transforms

    NASA Astrophysics Data System (ADS)

    Brown, Richard K.; Claypoole, Roger L., Jr.

    2001-12-01

    Imagery is collected much faster and in significantly greater quantities today compared to a few years ago. Accurate registration of this imagery is vital for comparing the similarities and differences between multiple images. Image registration is a significant component in computer vision and other pattern recognition problems, medical applications such as Medical Resonance Images (MRI) and Positron Emission Tomography (PET), remotely sensed data for target location and identification, and super-resolution algorithms. Since human analysis is tedious and error prone for large data sets, we require an automatic, efficient, robust, and accurate method to register images. Wavelet transforms have proven useful for a variety of signal and image processing tasks. In our research, we present a fundamentally new wavelet-based registration algorithm utilizing redundant transforms and a masking process to suppress the adverse effects of noise and improve processing efficiency. The shift-invariant wavelet transform is applied in translation estimation and a new rotation-invariant polar wavelet transform is effectively utilized in rotation estimation. We demonstrate the robustness of these redundant wavelet transforms for the registration of two images (i.e., translating or rotating an input image to a reference image), but extensions to larger data sets are feasible. We compare the registration accuracy of our redundant wavelet transforms to the critically sampled discrete wavelet transform using the Daubechies wavelet to illustrate the power of our algorithm in the presence of significant additive white Gaussian noise and strongly translated or rotated images.

  9. A multi-scale registration of urban aerial image with airborne lidar data

    NASA Astrophysics Data System (ADS)

    Huang, Shuo; Chen, Siying; Zhang, Yinchao; Guo, Pan; Chen, He

    2015-11-01

    This paper presented a multi-scale progressive registration method of airborne LiDAR data with aerial image. The cores of the proposed method lie in the coarse registration with road networks and the fine registration method using regularized building corners. During the two-stage registration, the exterior orientation parameters (EOP) are continually refined. By validation of the actual flight data of Dunhuang, the experimental result shows that the proposed method can obtain accurate results with low-precision initial EOP, also improve the automatic degree of registration.

  10. Ricci Flow-based Spherical Parameterization and Surface Registration.

    PubMed

    Chen, X; He, H; Zou, G; Zhang, X; Gu, X; Hua, J

    2013-09-01

    This paper presents an improved Euclidean Ricci flow method for spherical parameterization. We subsequently invent a scale space processing built upon Ricci energy to extract robust surface features for accurate surface registration. Since our method is based on the proposed Euclidean Ricci flow, it inherits the properties of Ricci flow such as conformality, robustness and intrinsicalness, facilitating efficient and effective surface mapping. Compared with other surface registration methods using curvature or sulci pattern, our method demonstrates a significant improvement for surface registration. In addition, Ricci energy can capture local differences for surface analysis as shown in the experiments and applications. PMID:24019739

  11. Onboard Image Registration from Invariant Features

    NASA Technical Reports Server (NTRS)

    Wang, Yi; Ng, Justin; Garay, Michael J.; Burl, Michael C

    2008-01-01

    This paper describes a feature-based image registration technique that is potentially well-suited for onboard deployment. The overall goal is to provide a fast, robust method for dynamically combining observations from multiple platforms into sensors webs that respond quickly to short-lived events and provide rich observations of objects that evolve in space and time. The approach, which has enjoyed considerable success in mainstream computer vision applications, uses invariant SIFT descriptors extracted at image interest points together with the RANSAC algorithm to robustly estimate transformation parameters that relate one image to another. Experimental results for two satellite image registration tasks are presented: (1) automatic registration of images from the MODIS instrument on Terra to the MODIS instrument on Aqua and (2) automatic stabilization of a multi-day sequence of GOES-West images collected during the October 2007 Southern California wildfires.

  12. Registration of Optical Data with High-Resolution SAR Data: a New Image Registration Solution

    NASA Astrophysics Data System (ADS)

    Bahr, T.; Jin, X.

    2013-04-01

    Accurate image-to-image registration is critical for many image processing workflows, including georeferencing, change detection, data fusion, image mosaicking, DEM extraction and 3D modeling. Users need a solution to generate tie points accurately and geometrically align the images automatically. To solve these requirements we developed the Hybrid Powered Auto-Registration Engine (HyPARE). HyPARE combines all available spatial reference information with a number of image registration approaches to improve the accuracy, performance, and automation of tie point generation and image registration. We demonstrate this approach by the registration of a Pléiades-1a image with a TerraSAR-X SpotLight image of Hannover, Germany. Registering images with different modalities is a known challenging problem; e.g. manual tie point collection is prone to error. The registration engine allows to generate tie points automatically, using an optimized mutual information-based matching method. It produces more accurate results than traditional correlation-based measures. In this example the resulting tie points are well distributed across the overlapping areas, even as the images have significant local feature differences.

  13. Mono- and multimodal registration of optical breast images

    NASA Astrophysics Data System (ADS)

    Pearlman, Paul C.; Adams, Arthur; Elias, Sjoerd G.; Mali, Willem P. Th. M.; Viergever, Max A.; Pluim, Josien P. W.

    2012-08-01

    Optical breast imaging offers the possibility of noninvasive, low cost, and high sensitivity imaging of breast cancers. Poor spatial resolution and a lack of anatomical landmarks in optical images of the breast make interpretation difficult and motivate registration and fusion of these data with subsequent optical images and other breast imaging modalities. Methods used for registration and fusion of optical breast images are reviewed. Imaging concerns relevant to the registration problem are first highlighted, followed by a focus on both monomodal and multimodal registration of optical breast imaging. Where relevant, methods pertaining to other imaging modalities or imaged anatomies are presented. The multimodal registration discussion concerns digital x-ray mammography, ultrasound, magnetic resonance imaging, and positron emission tomography.

  14. SU-E-J-122: The CBCT Dose Calculation Using a Patient Specific CBCT Number to Mass Density Conversion Curve Based On a Novel Image Registration and Organ Mapping Method in Head-And-Neck Radiation Therapy

    SciTech Connect

    Zhou, J; Lasio, G; Chen, S; Zhang, B; Langen, K; Prado, K; D’Souza, W; Yi, B; Huang, J

    2015-06-15

    Purpose: To develop a CBCT HU correction method using a patient specific HU to mass density conversion curve based on a novel image registration and organ mapping method for head-and-neck radiation therapy. Methods: There are three steps to generate a patient specific CBCT HU to mass density conversion curve. First, we developed a novel robust image registration method based on sparseness analysis to register the planning CT (PCT) and the CBCT. Second, a novel organ mapping method was developed to transfer the organs at risk (OAR) contours from the PCT to the CBCT and corresponding mean HU values of each OAR were measured in both the PCT and CBCT volumes. Third, a set of PCT and CBCT HU to mass density conversion curves were created based on the mean HU values of OARs and the corresponding mass density of the OAR in the PCT. Then, we compared our proposed conversion curve with the traditional Catphan phantom based CBCT HU to mass density calibration curve. Both curves were input into the treatment planning system (TPS) for dose calculation. Last, the PTV and OAR doses, DVH and dose distributions of CBCT plans are compared to the original treatment plan. Results: One head-and-neck cases which contained a pair of PCT and CBCT was used. The dose differences between the PCT and CBCT plans using the proposed method are −1.33% for the mean PTV, 0.06% for PTV D95%, and −0.56% for the left neck. The dose differences between plans of PCT and CBCT corrected using the CATPhan based method are −4.39% for mean PTV, 4.07% for PTV D95%, and −2.01% for the left neck. Conclusion: The proposed CBCT HU correction method achieves better agreement with the original treatment plan compared to the traditional CATPhan based calibration method.

  15. Towards an intercomparison of automated registration algorithms for multiple source remote sensing data

    NASA Technical Reports Server (NTRS)

    LeMoigne, Jacqueline; Xia, Wei; Chettri, Samir; El-Ghazawi, Tarek; Kaymaz, Emre; Lerner, Bao-Ting; Mareboyana, Manohar; Netanyahu, Nathan; Pierce, John; Raghavan, Srini; Tilton, James C.; Campbell, William J.; Cromp, Robert F.

    1997-01-01

    The first step in the integration of multiple data is registration, either relative image-to-image registration or absolute geo-registration, to a map or a fixed coordinate system. As the need for automating registration techniques is recognized, we feel that there is a need to survey all the registration methods which may be applicable to Earth and space science problems and to evaluate their performances on a large variety of existing remote sensing data as well as on simulated data of soon-to-be-flown instruments. In this paper we will describe: 1) the operational toolbox which we are developing and which will consist in some of the most important registration techniques; and 2) the quantitative intercomparison of the different methods, which will allow a user to select the desired registration technique based on this evaluation and the visualization of the registration results.

  16. Automatic parameter selection for multimodal image registration.

    PubMed

    Hahn, Dieter A; Daum, Volker; Hornegger, Joachim

    2010-05-01

    Over the past ten years similarity measures based on intensity distributions have become state-of-the-art in automatic multimodal image registration. An implementation for clinical usage has to support a plurality of images. However, a generally applicable parameter configuration for the number and sizes of histogram bins, optimal Parzen-window kernel widths or background thresholds cannot be found. This explains why various research groups present partly contradictory empirical proposals for these parameters. This paper proposes a set of data-driven estimation schemes for a parameter-free implementation that eliminates major caveats of heuristic trial and error. We present the following novel approaches: a new coincidence weighting scheme to reduce the influence of background noise on the similarity measure in combination with Max-Lloyd requantization, and a tradeoff for the automatic estimation of the number of histogram bins. These methods have been integrated into a state-of-the-art rigid registration that is based on normalized mutual information and applied to CT-MR, PET-MR, and MR-MR image pairs of the RIRE 2.0 database. We compare combinations of the proposed techniques to a standard implementation using default parameters, which can be found in the literature, and to a manual registration by a medical expert. Additionally, we analyze the effects of various histogram sizes, sampling rates, and error thresholds for the number of histogram bins. The comparison of the parameter selection techniques yields 25 approaches in total, with 114 registrations each. The number of bins has no significant influence on the proposed implementation that performs better than both the manual and the standard method in terms of acceptance rates and target registration error (TRE). The overall mean TRE is 2.34 mm compared to 2.54 mm for the manual registration and 6.48 mm for a standard implementation. Our results show a significant TRE reduction for distortion

  17. Highly accurate fast lung CT registration

    NASA Astrophysics Data System (ADS)

    Rühaak, Jan; Heldmann, Stefan; Kipshagen, Till; Fischer, Bernd

    2013-03-01

    Lung registration in thoracic CT scans has received much attention in the medical imaging community. Possible applications range from follow-up analysis, motion correction for radiation therapy, monitoring of air flow and pulmonary function to lung elasticity analysis. In a clinical environment, runtime is always a critical issue, ruling out quite a few excellent registration approaches. In this paper, a highly efficient variational lung registration method based on minimizing the normalized gradient fields distance measure with curvature regularization is presented. The method ensures diffeomorphic deformations by an additional volume regularization. Supplemental user knowledge, like a segmentation of the lungs, may be incorporated as well. The accuracy of our method was evaluated on 40 test cases from clinical routine. In the EMPIRE10 lung registration challenge, our scheme ranks third, with respect to various validation criteria, out of 28 algorithms with an average landmark distance of 0.72 mm. The average runtime is about 1:50 min on a standard PC, making it by far the fastest approach of the top-ranking algorithms. Additionally, the ten publicly available DIR-Lab inhale-exhale scan pairs were registered to subvoxel accuracy at computation times of only 20 seconds. Our method thus combines very attractive runtimes with state-of-the-art accuracy in a unique way.

  18. Registration Of SAR Images With Multisensor Images

    NASA Technical Reports Server (NTRS)

    Evans, Diane L.; Burnette, Charles F.; Van Zyl, Jakob J.

    1993-01-01

    Semiautomated technique intended primarily to facilitate registration of polarimetric synthetic-aperture-radar (SAR) images with other images of same or partly overlapping terrain while preserving polarization information conveyed by SAR data. Technique generally applicable in sense one or both of images to be registered with each other generated by polarimetric or nonpolarimetric SAR, infrared radiometry, conventional photography, or any other applicable sensing method.

  19. Automatic digital image registration

    NASA Technical Reports Server (NTRS)

    Goshtasby, A.; Jain, A. K.; Enslin, W. R.

    1982-01-01

    This paper introduces a general procedure for automatic registration of two images which may have translational, rotational, and scaling differences. This procedure involves (1) segmentation of the images, (2) isolation of dominant objects from the images, (3) determination of corresponding objects in the two images, and (4) estimation of transformation parameters using the center of gravities of objects as control points. An example is given which uses this technique to register two images which have translational, rotational, and scaling differences.

  20. Spacecraft camera image registration

    NASA Technical Reports Server (NTRS)

    Kamel, Ahmed A. (Inventor); Graul, Donald W. (Inventor); Chan, Fred N. T. (Inventor); Gamble, Donald W. (Inventor)

    1987-01-01

    A system for achieving spacecraft camera (1, 2) image registration comprises a portion external to the spacecraft and an image motion compensation system (IMCS) portion onboard the spacecraft. Within the IMCS, a computer (38) calculates an image registration compensation signal (60) which is sent to the scan control loops (84, 88, 94, 98) of the onboard cameras (1, 2). At the location external to the spacecraft, the long-term orbital and attitude perturbations on the spacecraft are modeled. Coefficients (K, A) from this model are periodically sent to the onboard computer (38) by means of a command unit (39). The coefficients (K, A) take into account observations of stars and landmarks made by the spacecraft cameras (1, 2) themselves. The computer (38) takes as inputs the updated coefficients (K, A) plus synchronization information indicating the mirror position (AZ, EL) of each of the spacecraft cameras (1, 2), operating mode, and starting and stopping status of the scan lines generated by these cameras (1, 2), and generates in response thereto the image registration compensation signal (60). The sources of periodic thermal errors on the spacecraft are discussed. The system is checked by calculating measurement residuals, the difference between the landmark and star locations predicted at the external location and the landmark and star locations as measured by the spacecraft cameras (1, 2).

  1. SU-E-J-112: Intensity-Based Pulmonary Image Registration: An Evaluation Study

    SciTech Connect

    Yang, F; Meyer, J; Sandison, G

    2015-06-15

    Purpose: Accurate alignment of thoracic CT images is essential for dose tracking and to safely implement adaptive radiotherapy in lung cancers. At the same time it is challenging given the highly elastic nature of lung tissue deformations. The objective of this study was to assess the performances of three state-of-art intensity-based algorithms in terms of their ability to register thoracic CT images subject to affine, barrel, and sinusoid transformation. Methods: Intensity similarity measures of the evaluated algorithms contained sum-of-squared difference (SSD), local mutual information (LMI), and residual complexity (RC). Five thoracic CT scans obtained from the EMPIRE10 challenge database were included and served as reference images. Each CT dataset was distorted by realistic affine, barrel, and sinusoid transformations. Registration performances of the three algorithms were evaluated for each distortion type in terms of intensity root mean square error (IRMSE) between the reference and registered images in the lung regions. Results: For affine distortions, the three algorithms differed significantly in registration of thoracic images both visually and nominally in terms of IRMSE with a mean of 0.011 for SSD, 0.039 for RC, and 0.026 for LMI (p<0.01; Kruskal-Wallis test). For barrel distortion, the three algorithms showed nominally no significant difference in terms of IRMSE with a mean of 0.026 for SSD, 0.086 for RC, and 0.054 for LMI (p=0.16) . A significant difference was seen for sinusoid distorted thoracic CT data with mean lung IRMSE of 0.039 for SSD, 0.092 for RC, and 0.035 for LMI (p=0.02). Conclusion: Pulmonary deformations might vary to a large extent in nature in a daily clinical setting due to factors ranging from anatomy variations to respiratory motion to image quality. It can be appreciated from the results of the present study that the suitability of application of a particular algorithm for pulmonary image registration is deformation-dependent.

  2. A surface-matching technique for robot-assisted registration.

    PubMed

    Glozman, D; Shoham, M; Fischer, A

    2001-01-01

    Successful implementation of robot-assisted surgery (RAS) requires coherent integration of spatial image data with sensing and actuating devices, each having its own coordinate system. Hence, accurate estimation of the geometric relationships between relevant reference frames, known as registration, is a crucial procedure in all RAS applications. The purpose of this paper is to present a new registration scheme, along with the results of an experimental evaluation of a robot-assisted registration method for RAS applications in orthopedics. The accuracy of the proposed registration is appropriate for specified orthopedic surgical applications such as Total Knee Replacement. The registration method is based on a surface-matching algorithm that does not require marker implants, thereby reducing surgical invasiveness. Points on the bone surface are sampled by the robot, which in turn directs the surgical tool. This technique eliminates additional coordinate transformations to an external device (such as a digitizer), resulting in increased surgical accuracy. The registration technique was tested on an RSPR six-degrees-of-freedom parallel robot specifically designed for medical applications. A six-axis force sensor attached to the robot's moving platform enables fast and accurate acquisition of positions and surface normal directions at sampled points. Sampling with a robot probe was shown to be accurate, fast, and easy to perform. The whole procedure takes about 2 min, with the robot performing most of the registration procedures, leaving the surgeon's hands free. Robotic registration was shown to provide a flawless link between preoperative planning and robotic assistance during surgery. PMID:11892002

  3. Color image registration based on quaternion Fourier transformation

    NASA Astrophysics Data System (ADS)

    Wang, Qiang; Wang, Zhengzhi

    2012-05-01

    The traditional Fourier Mellin transform is applied to quaternion algebra in order to investigate quaternion Fourier transformation properties useful for color image registration in frequency domain. Combining with the quaternion phase correlation, we propose a method for color image registration based on the quaternion Fourier transform. The registration method, which processes color image in a holistic manner, is convenient to realign color images differing in translation, rotation, and scaling. Experimental results on different types of color images indicate that the proposed method not only obtains high accuracy in similarity transform in the image plane but also is computationally efficient.

  4. Displacement phenomena in lectin affinity chromatography.

    PubMed

    Cho, Wonryeon

    2015-10-01

    The work described here examines displacement phenomena that play a role in lectin affinity chromatography and their potential to impact reproducibility. This was achieved using Lycopersicon esculentum lectin (LEL), a lectin widely used in monitoring cancer. Four small identical LEL columns were coupled in series to form a single affinity chromatography system with the last in the series connected to an absorbance detector. The serial affinity column set (SACS) was then loaded with human plasma proteins. At the completion of loading, the column set was disassembled, the four columns were eluted individually, the captured proteins were trypsin digested, the peptides were deglycosylated with PNGase F, and the parent proteins were identified through mass spectral analyses. Significantly different sets of glycoproteins were selected by each column, some proteins appearing to be exclusively bound to the first column while others were bound further along in the series. Clearly, sample displacement chromatography (SDC) occurs. Glycoproteins were bound at different places in the column train, identifying the presence of glycoforms with different affinity on a single glycoprotein. It is not possible to see these phenomena in the single column mode of chromatography. Moreover, low abundance proteins were enriched, which facilitates detection. The great advantage of this method is that it differentiates between glycoproteins on the basis of their binding affinity. Displacement phenomena are concluded to be a significant component of the separation mechanism in heavily loaded lectin affinity chromatography columns. This further suggests that care must be exercised in sample loading of lectin columns to prevent analyte displacement with nonretained proteins. PMID:26348026

  5. Hyperspectral Imaging for Cancer Surgical Margin Delineation: Registration of Hyperspectral and Histological Images

    PubMed Central

    Lu, Guolan; Halig, Luma; Wang, Dongsheng; Chen, Zhuo Georgia; Fei, Baowei

    2014-01-01

    The determination of tumor margins during surgical resection remains a challenging task. A complete removal of malignant tissue and conservation of healthy tissue is important for the preservation of organ function, patient satisfaction, and quality of life. Visual inspection and palpation is not sufficient for discriminating between malignant and normal tissue types. Hyperspectral imaging (HSI) technology has the potential to noninvasively delineate surgical tumor margin and can be used as an intra-operative visual aid tool. Since histological images provide the ground truth of cancer margins, it is necessary to warp the cancer regions in ex vivo histological images back to in vivo hyperspectral images in order to validate the tumor margins detected by HSI and to optimize the imaging parameters. In this paper, principal component analysis (PCA) is utilized to extract the principle component bands of the HSI images, which is then used to register HSI images with the corresponding histological image. Affine registration is chosen to model the global transformation. A B-spline free form deformation (FFD) method is used to model the local non-rigid deformation. Registration experiment was performed on animal hyperspectral and histological images. Experimental results from animals demonstrated the feasibility of the hyperspectral imaging method for cancer margin detection. PMID:25328640

  6. Hyperspectral imaging for cancer surgical margin delineation: registration of hyperspectral and histological images

    NASA Astrophysics Data System (ADS)

    Lu, Guolan; Halig, Luma; Wang, Dongsheng; Chen, Zhuo G.; Fei, Baowei

    2014-03-01

    The determination of tumor margins during surgical resection remains a challenging task. A complete removal of malignant tissue and conservation of healthy tissue is important for the preservation of organ function, patient satisfaction, and quality of life. Visual inspection and palpation is not sufficient for discriminating between malignant and normal tissue types. Hyperspectral imaging (HSI) technology has the potential to noninvasively delineate surgical tumor margin and can be used as an intra-operative visual aid tool. Since histological images provide the ground truth of cancer margins, it is necessary to warp the cancer regions in ex vivo histological images back to in vivo hyperspectral images in order to validate the tumor margins detected by HSI and to optimize the imaging parameters. In this paper, principal component analysis (PCA) is utilized to extract the principle component bands of the HSI images, which is then used to register HSI images with the corresponding histological image. Affine registration is chosen to model the global transformation. A B-spline free form deformation (FFD) method is used to model the local non-rigid deformation. Registration experiment was performed on animal hyperspectral and histological images. Experimental results from animals demonstrated the feasibility of the hyperspectral imaging method for cancer margin detection.

  7. Automatic thoracic anatomy segmentation on CT images using hierarchical fuzzy models and registration

    NASA Astrophysics Data System (ADS)

    Sun, Kaioqiong; Udupa, Jayaram K.; Odhner, Dewey; Tong, Yubing; Torigian, Drew A.

    2014-03-01

    This paper proposes a thoracic anatomy segmentation method based on hierarchical recognition and delineation guided by a built fuzzy model. Labeled binary samples for each organ are registered and aligned into a 3D fuzzy set representing the fuzzy shape model for the organ. The gray intensity distributions of the corresponding regions of the organ in the original image are recorded in the model. The hierarchical relation and mean location relation between different organs are also captured in the model. Following the hierarchical structure and location relation, the fuzzy shape model of different organs is registered to the given target image to achieve object recognition. A fuzzy connected delineation method is then used to obtain the final segmentation result of organs with seed points provided by recognition. The hierarchical structure and location relation integrated in the model provide the initial parameters for registration and make the recognition efficient and robust. The 3D fuzzy model combined with hierarchical affine registration ensures that accurate recognition can be obtained for both non-sparse and sparse organs. The results on real images are presented and shown to be better than a recently reported fuzzy model-based anatomy recognition strategy.

  8. Hyperspectral Imaging for Cancer Surgical Margin Delineation: Registration of Hyperspectral and Histological Images.

    PubMed

    Lu, Guolan; Halig, Luma; Wang, Dongsheng; Chen, Zhuo Georgia; Fei, Baowei

    2014-03-12

    The determination of tumor margins during surgical resection remains a challenging task. A complete removal of malignant tissue and conservation of healthy tissue is important for the preservation of organ function, patient satisfaction, and quality of life. Visual inspection and palpation is not sufficient for discriminating between malignant and normal tissue types. Hyperspectral imaging (HSI) technology has the potential to noninvasively delineate surgical tumor margin and can be used as an intra-operative visual aid tool. Since histological images provide the ground truth of cancer margins, it is necessary to warp the cancer regions in ex vivo histological images back to in vivo hyperspectral images in order to validate the tumor margins detected by HSI and to optimize the imaging parameters. In this paper, principal component analysis (PCA) is utilized to extract the principle component bands of the HSI images, which is then used to register HSI images with the corresponding histological image. Affine registration is chosen to model the global transformation. A B-spline free form deformation (FFD) method is used to model the local non-rigid deformation. Registration experiment was performed on animal hyperspectral and histological images. Experimental results from animals demonstrated the feasibility of the hyperspectral imaging method for cancer margin detection. PMID:25328640

  9. Registration of structurally dissimilar images in MRI-based brachytherapy

    NASA Astrophysics Data System (ADS)

    Berendsen, F. F.; Kotte, A. N. T. J.; de Leeuw, A. A. C.; Jürgenliemk-Schulz, I. M.; Viergever, M. A.; Pluim, J. P. W.

    2014-08-01

    A serious challenge in image registration is the accurate alignment of two images in which a certain structure is present in only one of the two. Such topological changes are problematic for conventional non-rigid registration algorithms. We propose to incorporate in a conventional free-form registration framework a geometrical penalty term that minimizes the volume of the missing structure in one image. We demonstrate our method on cervical MR images for brachytherapy. The intrapatient registration problem involves one image in which a therapy applicator is present and one in which it is not. By including the penalty term, a substantial improvement in the surface distance to the gold standard anatomical position and the residual volume of the applicator void are obtained. Registration of neighboring structures, i.e. the rectum and the bladder is generally improved as well, albeit to a lesser degree.

  10. An automatic nonrigid registration for stained histological sections.

    PubMed

    Auer, Martin; Regitnig, Peter; Holzapfel, Gerhard A

    2005-04-01

    Automatic computer-based analyses of histological sections which are differently stained require that they are related to each other. Most registration methods are only able to perform rigid-body motion and are sensitive to noise and artifacts. Histological images, however, are accompanied by several artifacts and different contrasts, which require a nonrigid registration. In this paper, we present a hierarchical nonrigid registration algorithm able to align images, which contain minor image artifacts. The algorithm requires no a priori knowledge of the true image. The hierarchical design of the algorithm enhances robustness and accuracy, and saves computational costs. The proposed algorithm is decomposed into a fast, coarse, rigid registration step and a slower, but finer, nonrigid step. For the coarse registration, we use image pyramids, while for the second step, we combine a point-based registration with an elastic thin-plate spline interpolation. Accuracy tests, performed for 20 histological images obtained from human arteries, have shown that the error measure is acceptable, and that the image noise does not cause a problem. The associated convergence rate of the mean pixel displacement error during the rigid and nonrigid registrations is satisfying. The algorithm can be applied to various multicontrast elastic registration problems in medical imaging and may be extended to three dimensions. PMID:15825482

  11. Diffeomorphic Registration of Images with Variable Contrast Enhancement

    PubMed Central

    Janssens, Guillaume; Jacques, Laurent; Orban de Xivry, Jonathan; Geets, Xavier; Macq, Benoit

    2011-01-01

    Nonrigid image registration is widely used to estimate tissue deformations in highly deformable anatomies. Among the existing methods, nonparametric registration algorithms such as optical flow, or Demons, usually have the advantage of being fast and easy to use. Recently, a diffeomorphic version of the Demons algorithm was proposed. This provides the advantage of producing invertible displacement fields, which is a necessary condition for these to be physical. However, such methods are based on the matching of intensities and are not suitable for registering images with different contrast enhancement. In such cases, a registration method based on the local phase like the Morphons has to be used. In this paper, a diffeomorphic version of the Morphons registration method is proposed and compared to conventional Morphons, Demons, and diffeomorphic Demons. The method is validated in the context of radiotherapy for lung cancer patients on several 4D respiratory-correlated CT scans of the thorax with and without variable contrast enhancement. PMID:21197460

  12. Lung registration using airway tree morphometry

    NASA Astrophysics Data System (ADS)

    Tan, Jun; Zheng, Bin; Park, Sang; Pu, Jiantao; Wenzel, Sally E.; Leader, Joseph K.

    2011-03-01

    This paper describes a non-linear medical image registration algorithm that aligns lung CT images scanned at different respiratory phases. The method uses landmarks obtained from the airway tree to find the airway branch extension lines and where the lines intersect the lung surface. The branch extension and lung intersection voxels on the surface were the crucial landmarks that initialize the non-rigid registration process. The advantage of these landmarks is that they have high correspondence between the matching patterns in the template images and deformed images. This method was developed and tested on CT examinations from participants in an asthma study. The registration accuracy was evaluated by the average distance between the corresponding airway tree branch points in the pair of images. The mean value of the distance between landmarks in template images and deformed matching images for subjects 1 and 2 were 8.44 mm (+/-4.46 mm) and 4.33 mm (+/- 3.78 mm), respectively. The results show that the lung image registration technique developed in this study may prove useful in quantifying longitudinal changes, performing regional analysis, tracking lung tumors, and compensating for subject motion across CT images.

  13. Inter-slice bidirectional registration-based segmentation of the prostate gland in MR and CT image sequences

    SciTech Connect

    Khalvati, Farzad Tizhoosh, Hamid R.; Salmanpour, Aryan; Rahnamayan, Shahryar; Rodrigues, George

    2013-12-15

    Purpose: Accurate segmentation and volume estimation of the prostate gland in magnetic resonance (MR) and computed tomography (CT) images are necessary steps in diagnosis, treatment, and monitoring of prostate cancer. This paper presents an algorithm for the prostate gland volume estimation based on the semiautomated segmentation of individual slices in T2-weighted MR and CT image sequences. Methods: The proposedInter-Slice Bidirectional Registration-based Segmentation (iBRS) algorithm relies on interslice image registration of volume data to segment the prostate gland without the use of an anatomical atlas. It requires the user to mark only three slices in a given volume dataset, i.e., the first, middle, and last slices. Next, the proposed algorithm uses a registration algorithm to autosegment the remaining slices. We conducted comprehensive experiments to measure the performance of the proposed algorithm using three registration methods (i.e., rigid, affine, and nonrigid techniques). Results: The results with the proposed technique were compared with manual marking using prostate MR and CT images from 117 patients. Manual marking was performed by an expert user for all 117 patients. The median accuracies for individual slices measured using the Dice similarity coefficient (DSC) were 92% and 91% for MR and CT images, respectively. The iBRS algorithm was also evaluated regarding user variability, which confirmed that the algorithm was robust to interuser variability when marking the prostate gland. Conclusions: The proposed algorithm exploits the interslice data redundancy of the images in a volume dataset of MR and CT images and eliminates the need for an atlas, minimizing the computational cost while producing highly accurate results which are robust to interuser variability.

  14. 14 CFR 47.43 - Invalid registration.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 1 2011-01-01 2011-01-01 false Invalid registration. 47.43 Section 47.43... REGISTRATION Certificates of Aircraft Registration § 47.43 Invalid registration. Link to an amendment published... registration of an aircraft is invalid if, at the time it is made— (1) The aircraft is registered in a...

  15. 17 CFR 250.1 - Registration.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 17 Commodity and Securities Exchanges 3 2011-04-01 2011-04-01 false Registration. 250.1 Section... AND REGULATIONS, PUBLIC UTILITY HOLDING COMPANY ACT OF 1935 Registration and General Exemptions § 250.1 Registration. (a) Notification of registration. Notifications of registration pursuant to...

  16. 17 CFR 250.1 - Registration.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Registration. 250.1 Section... AND REGULATIONS, PUBLIC UTILITY HOLDING COMPANY ACT OF 1935 Registration and General Exemptions § 250.1 Registration. (a) Notification of registration. Notifications of registration pursuant to...

  17. Improved native affinity purification of RNA.

    PubMed

    Batey, Robert T; Kieft, Jeffrey S

    2007-08-01

    RNA biochemical or structural studies often require an RNA sample that is chemically pure, and most protocols for its in vitro production use denaturing polyacrylamide gel electrophoresis to achieve this. Unfortunately, many RNAs do not quantitatively refold into an active conformation after denaturation, creating significant problems for downstream characterization or use. In addition, this traditional purification method is not amenable to studies demanding high-throughput RNA production. Recently, we presented the first general method for producing almost any RNA sequence that employs an affinity tag that is removed during the purification process. Because technical difficulties prevented application of this method to many RNAs, we have developed an improved version that utilizes a different activatable ribozyme and affinity tag that are considerably more robust, rapid, and broadly applicable. PMID:17548432

  18. An image registration based ultrasound probe calibration

    NASA Astrophysics Data System (ADS)

    Li, Xin; Kumar, Dinesh; Sarkar, Saradwata; Narayanan, Ram

    2012-02-01

    Reconstructed 3D ultrasound of prostate gland finds application in several medical areas such as image guided biopsy, therapy planning and dose delivery. In our application, we use an end-fire probe rotated about its axis to acquire a sequence of rotational slices to reconstruct 3D TRUS (Transrectal Ultrasound) image. The image acquisition system consists of an ultrasound transducer situated on a cradle directly attached to a rotational sensor. However, due to system tolerances, axis of probe does not align exactly with the designed axis of rotation resulting in artifacts in the 3D reconstructed ultrasound volume. We present a rigid registration based automatic probe calibration approach. The method uses a sequence of phantom images, each pair acquired at angular separation of 180 degrees and registers corresponding image pairs to compute the deviation from designed axis. A modified shadow removal algorithm is applied for preprocessing. An attribute vector is constructed from image intensity and a speckle-insensitive information-theoretic feature. We compare registration between the presented method and expert-corrected images in 16 prostate phantom scans. Images were acquired at multiple resolutions, and different misalignment settings from two ultrasound machines. Screenshots from 3D reconstruction are shown before and after misalignment correction. Registration parameters from automatic and manual correction were found to be in good agreement. Average absolute differences of translation and rotation between automatic and manual methods were 0.27 mm and 0.65 degree, respectively. The registration parameters also showed lower variability for automatic registration (pooled standard deviation σtranslation = 0.50 mm, σrotation = 0.52 degree) compared to the manual approach (pooled standard deviation σtranslation = 0.62 mm, σrotation = 0.78 degree).

  19. Combined Volumetric and Surface Registration

    PubMed Central

    Zöllei, Lilla; Fischl, Bruce

    2009-01-01

    In this paper, we propose a novel method for the registration of volumetric images of the brain that optimizes the alignment of both cortical and subcortical structures. In order to achieve this, relevant geometrical information is extracted from a surface-based morph and diffused into the volume using the Navier operator of elasticity, resulting in a volumetric warp that aligns cortical folding patterns. This warp field is then refined with an intensity driven optical flow procedure that registers noncortical regions, while preserving the cortical alignment. The result is a combined surface and volume morph (CVS) that accurately registers both cortical and subcortical regions, establishing a single coordinate system suitable for the entire brain. PMID:19273000

  20. Quantifying brain development in early childhood using segmentation and registration

    NASA Astrophysics Data System (ADS)

    Aljabar, P.; Bhatia, K. K.; Murgasova, M.; Hajnal, J. V.; Boardman, J. P.; Srinivasan, L.; Rutherford, M. A.; Dyet, L. E.; Edwards, A. D.; Rueckert, D.

    2007-03-01

    In this work we obtain estimates of tissue growth using longitudinal data comprising MR brain images of 25 preterm children scanned at one and two years. The growth estimates are obtained using segmentation and registration based methods. The segmentation approach used an expectation maximisation (EM) method to classify tissue types and the registration approach used tensor based morphometry (TBM) applied to a free form deformation (FFD) model. The two methods show very good agreement indicating that the registration and segmentation approaches can be used interchangeably. The advantage of the registration based method, however, is that it can provide more local estimates of tissue growth. This is the first longitudinal study of growth in early childhood, previous longitudinal studies have focused on later periods during childhood.

  1. Fast interactive registration tool for reproducible multi-spectral imaging for wound healing and treatment evaluation

    NASA Astrophysics Data System (ADS)

    Noordmans, Herke J.; de Roode, Rowland; Verdaasdonk, Rudolf

    2007-02-01

    Multi-spectral images of human tissue taken in-vivo often contain image alignment problems as patients have difficulty in retaining their posture during the acquisition time of 20 seconds. Previously, it has been attempted to correct motion errors with image registration software developed for MR or CT data but these algorithms have been proven to be too slow and erroneous for practical use with multi-spectral images. A new software package has been developed which allows the user to play a decisive role in the registration process as the user can monitor the progress of the registration continuously and force it in the right direction when it starts to fail. The software efficiently exploits videocard hardware to gain speed and to provide a perfect subvoxel correspondence between registration field and display. An 8 bit graphic card was used to efficiently register and resample 12 bit images using the hardware interpolation modes present on the graphic card. To show the feasibility of this new registration process, the software was applied in clinical practice evaluating the dosimetry for psoriasis and KTP laser treatment. The microscopic differences between images of normal skin and skin exposed to UV light proved that an affine registration step including zooming and slanting is critical for a subsequent elastic match to have success. The combination of user interactive registration software with optimal addressing the potentials of PC video card hardware greatly improves the speed of multi spectral image registration.

  2. An intensity-based approach to x-ray mammography: MRI registration

    NASA Astrophysics Data System (ADS)

    Mertzanidou, Thomy; Hipwell, John H.; Tanner, Christine; Hawkes, David J.

    2010-03-01

    This paper presents a novel approach to X-ray mammography - MRI registration. The proposed method uses an intensity-based technique and an affine transformation matrix to approximate the 3D deformation of the breast resulting from the compression applied during mammogram acquisition. The registration is driven by a similarity measure that is calculated at each iteration of the algorithm between the target X-ray mammogram and a simulated X-ray image, created from the MR volume. Although the similarity measure is calculated in 2D, we compute a 3D transformation that is updated at each iteration. We have performed two types of experiments. In the first set, we used simulated X-ray target data, for which the ground truth deformation of the volume was known and thus the results could be validated. For this case, we examined the performance of 4 different similarity measures and we show that Normalized Cross Correlation and Gradient Difference perform best. The calculated mean reprojection error was for both similarity measures 4mm, for an initial misregistration of 14mm. In the second set of experiments, we present the initial results of registering real X-ray mammograms with MR volumes. The results indicate that the breast boundaries were registered well and the volume was deformed in 3D in a similar way to the deformation of the breast during X-ray mammogram acquisition. The experiments were carried out on five patients.

  3. Open-source image registration for MRI–TRUS fusion-guided prostate interventions

    PubMed Central

    Khallaghi, Siavash; Sánchez, C. Antonio; Lasso, Andras; Fels, Sidney; Tuncali, Kemal; Sugar, Emily Neubauer; Kapur, Tina; Zhang, Chenxi; Wells, William; Nguyen, Paul L.; Abolmaesumi, Purang; Tempany, Clare

    2015-01-01

    Purpose We propose two software tools for non-rigid registration of MRI and transrectal ultrasound (TRUS) images of the prostate. Our ultimate goal is to develop an open-source solution to support MRI–TRUS fusion image guidance of prostate interventions, such as targeted biopsy for prostate cancer detection and focal therapy. It is widely hypothesized that image registration is an essential component in such systems. Methods The two non-rigid registration methods are: (1) a deformable registration of the prostate segmentation distance maps with B-spline regularization and (2) a finite element-based deformable registration of the segmentation surfaces in the presence of partial data. We evaluate the methods retrospectively using clinical patient image data collected during standard clinical procedures. Computation time and Target Registration Error (TRE) calculated at the expert-identified anatomical landmarks were used as quantitative measures for the evaluation. Results The presented image registration tools were capable of completing deformable registration computation within 5 min. Average TRE was approximately 3 mm for both methods, which is comparable with the slice thickness in our MRI data. Both tools are available under nonrestrictive open-source license. Conclusions We release open-source tools that may be used for registration during MRI–TRUS-guided prostate interventions. Our tools implement novel registration approaches and produce acceptable registration results. We believe these tools will lower the barriers in development and deployment of interventional research solutions and facilitate comparison with similar tools. PMID:25847666

  4. Reflectance and fluorescence hyperspectral elastic image registration

    NASA Astrophysics Data System (ADS)

    Lange, Holger; Baker, Ross; Hakansson, Johan; Gustafsson, Ulf P.

    2004-05-01

    Science and Technology International (STI) presents a novel multi-modal elastic image registration approach for a new hyperspectral medical imaging modality. STI's HyperSpectral Diagnostic Imaging (HSDI) cervical instrument is used for the early detection of uterine cervical cancer. A Computer-Aided-Diagnostic (CAD) system is being developed to aid the physician with the diagnosis of pre-cancerous and cancerous tissue regions. The CAD system uses the fusion of multiple data sources to optimize its performance. The key enabling technology for the data fusion is image registration. The difficulty lies in the image registration of fluorescence and reflectance hyperspectral data due to the occurrence of soft tissue movement and the limited resemblance of these types of imagery. The presented approach is based on embedding a reflectance image in the fluorescence hyperspectral imagery. Having a reflectance image in both data sets resolves the resemblance problem and thereby enables the use of elastic image registration algorithms required to compensate for soft tissue movements. Several methods of embedding the reflectance image in the fluorescence hyperspectral imagery are described. Initial experiments with human subject data are presented where a reflectance image is embedded in the fluorescence hyperspectral imagery.

  5. Analysis of biomolecular interactions using affinity microcolumns: A review

    PubMed Central

    Zheng, Xiwei; Li, Zhao; Beeram, Sandya; Podariu, Maria; Matsuda, Ryan; Pfaunmiller, Erika L.; White, Christopher J.; Carter, NaTasha; Hage, David S.

    2014-01-01

    Affinity chromatography has become an important tool for characterizing biomolecular interactions. The use of affinity microcolumns, which contain immobilized binding agents and have volumes in the mid-to-low microliter range, has received particular attention in recent years. Potential advantages of affinity microcolumns include the many analysis and detection formats that can be used with these columns, as well as the need for only small amounts of supports and immobilized binding agents. This review examines how affinity microcolumns have been used to examine biomolecular interactions. Both capillary-based microcolumns and short microcolumns are considered. The use of affinity microcolumns with zonal elution and frontal analysis methods are discussed. The techniques of peak decay analysis, ultrafast affinity extraction, split-peak analysis, and band-broadening studies are also explored. The principles of these methods are examined and various applications are provided to illustrate the use of these methods with affinity microcolumns. It is shown how these techniques can be utilized to provide information on the binding strength and kinetics of an interaction, as well as on the number and types of binding sites. It is further demonstrated how information on competition or displacement effects can be obtained by these methods. PMID:24572459

  6. Analysis of biomolecular interactions using affinity microcolumns: a review.

    PubMed

    Zheng, Xiwei; Li, Zhao; Beeram, Sandya; Podariu, Maria; Matsuda, Ryan; Pfaunmiller, Erika L; White, Christopher J; Carter, NaTasha; Hage, David S

    2014-10-01

    Affinity chromatography has become an important tool for characterizing biomolecular interactions. The use of affinity microcolumns, which contain immobilized binding agents and have volumes in the mid-to-low microliter range, has received particular attention in recent years. Potential advantages of affinity microcolumns include the many analysis and detection formats that can be used with these columns, as well as the need for only small amounts of supports and immobilized binding agents. This review examines how affinity microcolumns have been used to examine biomolecular interactions. Both capillary-based microcolumns and short microcolumns are considered. The use of affinity microcolumns with zonal elution and frontal analysis methods are discussed. The techniques of peak decay analysis, ultrafast affinity extraction, split-peak analysis, and band-broadening studies are also explored. The principles of these methods are examined and various applications are provided to illustrate the use of these methods with affinity microcolumns. It is shown how these techniques can be utilized to provide information on the binding strength and kinetics of an interaction, as well as on the number and types of binding sites. It is further demonstrated how information on competition or displacement effects can be obtained by these methods. PMID:24572459

  7. Computer Assisted Operations: Registration Records, Schedules

    ERIC Educational Resources Information Center

    College and University, 1977

    1977-01-01

    Proceedings of AACRAO's 63rd annual meeting cover: computer networking in small colleges; continuous registration; computer logic; computerized academic record overview; on-line registration systems; and analysis of registration and records systems. (LBH)

  8. [Progresses in screening active compounds from herbal medicine by affinity chromatography].

    PubMed

    Feng, Ying-shu; Tong, Shan-shan; Xu, Xi-ming; Yu, Jiang-nan

    2015-03-01

    Affinity chromatography is a chromatographic method for separating molecules using the binding characteristics of the stationary phase with potential drug molecules. This method can be performed as a high throughput screening method and a chromatographic separation method to screen a variety of active drugs. This paper summarizes the history of affinity chromatography, screening technology of affinity chromatography, and application of affinity chromatography in screening bio-active compounds in herbal medicines, and then discusses its application prospects, in order to broaden applications of the affinity chromatography in drug screening. PMID:26226740

  9. Affinity Monolith-Integrated Microchips for Protein Purification and Concentration.

    PubMed

    Gao, Changlu; Sun, Xiuhua; Wang, Huaixin; Qiao, Wei; Hu, Bo

    2016-01-01

    Affinity chromatography is a valuable method to purify and concentrate minute amount of proteins. Monoliths with epoxy groups for affinity immobilization were prepared by direct in-situ photopolymerization of glycidyl methacrylate and ethylene glycol dimethacrylate in porogenic solvents consisting of 1-dodecanol and cyclohexanol. By integrating affinity monoliths onto a microfluidic system, targeted biomolecules can be captured and retained on affinity column, while other biomolecules having no specific interactions toward the immobilized ligands flow through the microchannel. Therefore, proteins which remain on the affinity column are purified and concentrated, and then eluted by appropriate solutions and finally, separated by microchip capillary electrophoresis. This integrated microfluidic device has been applied to the purification and separation of specific proteins (FITC-labeled human serum albumin and IgG) in a mixture. PMID:27473483

  10. Coarse Point Cloud Registration by Egi Matching of Voxel Clusters

    NASA Astrophysics Data System (ADS)

    Wang, Jinhu; Lindenbergh, Roderik; Shen, Yueqian; Menenti, Massimo

    2016-06-01

    Laser scanning samples the surface geometry of objects efficiently and records versatile information as point clouds. However, often more scans are required to fully cover a scene. Therefore, a registration step is required that transforms the different scans into a common coordinate system. The registration of point clouds is usually conducted in two steps, i.e. coarse registration followed by fine registration. In this study an automatic marker-free coarse registration method for pair-wise scans is presented. First the two input point clouds are re-sampled as voxels and dimensionality features of the voxels are determined by principal component analysis (PCA). Then voxel cells with the same dimensionality are clustered. Next, the Extended Gaussian Image (EGI) descriptor of those voxel clusters are constructed using significant eigenvectors of each voxel in the cluster. Correspondences between clusters in source and target data are obtained according to the similarity between their EGI descriptors. The random sampling consensus (RANSAC) algorithm is employed to remove outlying correspondences until a coarse alignment is obtained. If necessary, a fine registration is performed in a final step. This new method is illustrated on scan data sampling two indoor scenarios. The results of the tests are evaluated by computing the point to point distance between the two input point clouds. The presented two tests resulted in mean distances of 7.6 mm and 9.5 mm respectively, which are adequate for fine registration.

  11. Promoting Competence Through Voter Registration.

    ERIC Educational Resources Information Center

    Hanrahan, Mary; And Others

    1986-01-01

    Describes a voter registration drive undertaken by a department of social work within a major medical teaching hospital. Provides highlights of the registration effort and several clinical vignettes that illustrate the meaning of the drive to psychiatric patients. Implications for social work and for the education of social work trainees are…

  12. A Method to Site-Specifically Identify and Quantitate Carbonyl End Products of Protein Oxidation Using Oxidation-Dependent Element Coded Affinity Tags (O-ECAT) and NanoLiquid Chromatography Fourier Transform Mass Spectrometry

    SciTech Connect

    Lee, S; Young, N L; Whetstone, P A; Cheal, S M; Benner, W H; Lebrilla, C B; Meares, C F

    2005-08-25

    Protein oxidation is linked to cellular stress, aging, and disease. Protein oxidations that result in reactive species are of particular interest, since these reactive oxidation products may react with other proteins or biomolecules in an unmediated and irreversible fashion, providing a potential marker for a variety of disease mechanisms. We have developed a novel system to identify and quantitate, relative to other states, the sites of oxidation on a given protein. A specially designed Oxidation-dependent carbonyl-specific Element-Coded Affinity Mass Tag (O-ECAT), AOD, ((S)-2-(4-(2-aminooxy)-acetamido)-benzyl)-1, 4, 7, 10-tetraazacyclododecane-N, N', N'', N'''-tetraacetic acid, is used to covalently tag the residues of a protein oxidized to aldehyde or keto end products. After proteolysis, the resulting AOD-tagged peptides are affinity purified, and analyzed by nanoLC-FTICR-MS, which provides high specificity in extracting co-eluting AOD mass pairs with a unique mass difference and affords relative quantitation based on isotopic ratios. Using this methodology, we have mapped the surface oxidation sites on a model protein, recombinant human serum albumin (rHSA) in its native form (as purchased) and after FeEDTA oxidation. A variety of modified amino acid residues including lysine, arginine, proline, histidine, threonine, aspartic and glutamic acids, were found to be oxidized to aldehyde and keto end products. The sensitivity of this methodology is shown by the number of peptides identified, twenty peptides on the native protein and twenty-nine after surface oxidation using FeEDTA and ascorbate. All identified peptides map to the surface of the HSA crystal structure validating this method for identifying oxidized amino acids on protein surfaces. In relative quantitation experiments between FeEDTA oxidation and native protein oxidation, identified sites showed different relative propensities towards oxidation independent of amino acid residue. We expect to extend

  13. Target error for image-to-physical space registration: preliminary clinical results using laser range scanning

    NASA Astrophysics Data System (ADS)

    Cao, Aize; Miga, Michael I.; Dumpuri, P.; Ding, S.; Dawant, B. M.; Thompson, R. C.

    2007-03-01

    In this paper, preliminary results from an image-to-physical space registration platform are presented. The current platform employs traditional and novel methods of registration which use a variety of data sources to include: traditional synthetic skin-fiducial point-based registration, surface registration based on facial contours, brain feature point-based registration, brain vessel-to-vessel registration, and a more comprehensive cortical surface registration method that utilizes both geometric and intensity information from both the image volume and physical patient. The intraoperative face and cortical surfaces were digitized using a laser range scanner (LRS) capable of producing highly resolved textured point clouds. In two in vivo cases, a series of registrations were performed using these techniques and compared within the context of a true target error. One of the advantages of using a textured point cloud data stream is that true targets among the physical cortical surface and the preoperative image volume can be identified and used to assess image-to-physical registration methods. The results suggest that iterative closest point (ICP) method for intraoperative face surface registration is equivalent to point-based registration (PBR) method of skin fiducial markers. With regard to the initial image and physical space registration, for patient 1, mean target registration error (TRE) were 3.1+/-0.4 mm and 3.6 +/-0.9 mm for face ICP and skin fiducial PBR, respectively. For patient 2, the mean TRE were 5.7 +/-1.3 mm, and 6.6 +/-0.9 mm for face ICP and skin fiducial PBR, respectively. With regard to intraoperative cortical surface registration, SurfaceMI outperformed feature based PBR and vessel ICP with 1.7+/-1.8 mm for patient 1. For patient 2, the best result was achieved by using vessel ICP with 1.9+/-0.5 mm.

  14. Automatic registration of satellite imagery

    NASA Technical Reports Server (NTRS)

    Fonseca, Leila M. G.; Costa, Max H. M.; Manjunath, B. S.; Kenney, C.

    1997-01-01

    Image registration is one of the basic image processing operations in remote sensing. With the increase in the number of images collected every day from different sensors, automated registration of multi-sensor/multi-spectral images has become an important issue. A wide range of registration techniques has been developed for many different types of applications and data. The objective of this paper is to present an automatic registration algorithm which uses a multiresolution analysis procedure based upon the wavelet transform. The procedure is completely automatic and relies on the grey level information content of the images and their local wavelet transform modulus maxima. The registration algorithm is very simple and easy to apply because it needs basically one parameter. We have obtained very encouraging results on test data sets from the TM and SPOT sensor images of forest, urban and agricultural areas.

  15. A hybrid framework of multiple active appearance models and global registration for 3D prostate segmentation in MRI

    NASA Astrophysics Data System (ADS)

    Ghose, Soumya; Oliver, Arnau; Martí, Robert; Lladó, Xavier; Freixenet, Jordi; Mitra, Jhimli; Vilanova, Joan C.; Meriaudeau, Fabrice

    2012-02-01

    Real-time fusion of Magnetic Resonance (MR) and Trans Rectal Ultra Sound (TRUS) images aid in the localization of malignant tissues in TRUS guided prostate biopsy. Registration performed on segmented contours of the prostate reduces computational complexity and improves the multimodal registration accuracy. However, accurate and computationally efficient 3D segmentation of the prostate in MR images could be a challenging task due to inter-patient shape and intensity variability of the prostate gland. In this work, we propose to use multiple statistical shape and appearance models to segment the prostate in 2D and a global registration framework to impose shape restriction in 3D. Multiple mean parametric models of the shape and appearance corresponding to the apex, central and base regions of the prostate gland are derived from principal component analysis (PCA) of prior shape and intensity information of the prostate from the training data. The estimated parameters are then modified with the prior knowledge of the optimization space to achieve segmentation in 2D. The 2D segmented slices are then rigidly registered with the average 3D model produced by affine registration of the ground truth of the training datasets to minimize pose variations and impose 3D shape restriction. The proposed method achieves a mean Dice similarity coefficient (DSC) value of 0.88+/-0.11, and mean Hausdorff distance (HD) of 3.38+/-2.81 mm when validated with 15 prostate volumes of a public dataset in leave-one-out validation framework. The results achieved are better compared to some of the works in the literature.

  16. Homographic Patch Feature Transform: A Robustness Registration for Gastroscopic Surgery

    PubMed Central

    Wang, Bin; Liu, Jiquan; Duan, Huilong; Dai, Ning; Si, Jianmin

    2016-01-01

    Image registration is a key component of computer assistance in image guided surgery, and it is a challenging topic in endoscopic environments. In this study, we present a method for image registration named Homographic Patch Feature Transform (HPFT) to match gastroscopic images. HPFT can be used for tracking lesions and augmenting reality applications during gastroscopy. Furthermore, an overall evaluation scheme is proposed to validate the precision, robustness and uniformity of the registration results, which provides a standard for rejection of false matching pairs from corresponding results. Finally, HPFT is applied for processing in vivo gastroscopic data. The experimental results show that HPFT has stable performance in gastroscopic applications. PMID:27054567

  17. Is It Reliable to Use Common Molecular Docking Methods for Comparing the Binding Affinities of Enantiomer Pairs for Their Protein Target?

    PubMed Central

    Ramírez, David; Caballero, Julio

    2016-01-01

    Molecular docking is a computational chemistry method which has become essential for the rational drug design process. In this context, it has had great impact as a successful tool for the study of ligand–receptor interaction modes, and for the exploration of large chemical datasets through virtual screening experiments. Despite their unquestionable merits, docking methods are not reliable for predicting binding energies due to the simple scoring functions they use. However, comparisons between two or three complexes using the predicted binding energies as a criterion are commonly found in the literature. In the present work we tested how wise is it to trust the docking energies when two complexes between a target protein and enantiomer pairs are compared. For this purpose, a ligand library composed by 141 enantiomeric pairs was used, including compounds with biological activities reported against seven protein targets. Docking results using the software Glide (considering extra precision (XP), standard precision (SP), and high-throughput virtual screening (HTVS) modes) and AutoDock Vina were compared with the reported biological activities using a classification scheme. Our test failed for all modes and targets, demonstrating that an accurate prediction when binding energies of enantiomers are compared using docking may be due to chance. We also compared pairs of compounds with different molecular weights and found the same results. PMID:27104528

  18. Is It Reliable to Use Common Molecular Docking Methods for Comparing the Binding Affinities of Enantiomer Pairs for Their Protein Target?

    PubMed

    Ramírez, David; Caballero, Julio

    2016-01-01

    Molecular docking is a computational chemistry method which has become essential for the rational drug design process. In this context, it has had great impact as a successful tool for the study of ligand-receptor interaction modes, and for the exploration of large chemical datasets through virtual screening experiments. Despite their unquestionable merits, docking methods are not reliable for predicting binding energies due to the simple scoring functions they use. However, comparisons between two or three complexes using the predicted binding energies as a criterion are commonly found in the literature. In the present work we tested how wise is it to trust the docking energies when two complexes between a target protein and enantiomer pairs are compared. For this purpose, a ligand library composed by 141 enantiomeric pairs was used, including compounds with biological activities reported against seven protein targets. Docking results using the software Glide (considering extra precision (XP), standard precision (SP), and high-throughput virtual screening (HTVS) modes) and AutoDock Vina were compared with the reported biological activities using a classification scheme. Our test failed for all modes and targets, demonstrating that an accurate prediction when binding energies of enantiomers are compared using docking may be due to chance. We also compared pairs of compounds with different molecular weights and found the same results. PMID:27104528

  19. The Insight ToolKit image registration framework

    PubMed Central

    Avants, Brian B.; Tustison, Nicholas J.; Stauffer, Michael; Song, Gang; Wu, Baohua; Gee, James C.

    2014-01-01

    Publicly available scientific resources help establish evaluation standards, provide a platform for teaching and improve reproducibility. Version 4 of the Insight ToolKit (ITK4) seeks to establish new standards in publicly available image registration methodology. ITK4 makes several advances in comparison to previous versions of ITK. ITK4 supports both multivariate images and objective functions; it also unifies high-dimensional (deformation field) and low-dimensional (affine) transformations with metrics that are reusable across transform types and with composite transforms that allow arbitrary series of geometric mappings to be chained together seamlessly. Metrics and optimizers take advantage of multi-core resources, when available. Furthermore, ITK4 reduces the parameter optimization burden via principled heuristics that automatically set scaling across disparate parameter types (rotations vs. translations). A related approach also constrains steps sizes for gradient-based optimizers. The result is that tuning for different metrics and/or image pairs is rarely necessary allowing the researcher to more easily focus on design/comparison of registration strategies. In total, the ITK4 contribution is intended as a structure to support reproducible research practices, will provide a more extensive foundation against which to evaluate new work in image registration and also enable application level programmers a broad suite of tools on which to build. Finally, we contextualize this work with a reference registration evaluation study with application to pediatric brain labeling.1 PMID:24817849

  20. Serial Scanning and Registration of High Resolution Quantitative Computed Tomography Volume Scans for the Determination of Local Bone Density Changes

    NASA Technical Reports Server (NTRS)

    Whalen, Robert T.; Napel, Sandy; Yan, Chye H.

    1996-01-01

    Progress in development of the methods required to study bone remodeling as a function of time is reported. The following topics are presented: 'A New Methodology for Registration Accuracy Evaluation', 'Registration of Serial Skeletal Images for Accurately Measuring Changes in Bone Density', and 'Precise and Accurate Gold Standard for Multimodality and Serial Registration Method Evaluations.'

  1. INTER-GROUP IMAGE REGISTRATION BY HIERARCHICAL GRAPH SHRINKAGE

    PubMed Central

    Ying, Shihui; Wu, Guorong; Liao, Shu; Shen, Dinggang

    2013-01-01

    In this paper, we propose a novel inter-group image registration method to register different groups of images (e.g., young and elderly brains) simultaneously. Specifically, we use a hierarchical two-level graph to model the distribution of entire images on the manifold, with intra-graph representing the image distribution in each group and the inter-graph describing the relationship between two groups. Then the procedure of inter-group registration is formulated as a dynamic evolution of graph shrinkage. The advantage of our method is that the topology of entire image distribution is explored to guide the image registration. In this way, each image coordinates with its neighboring images on the manifold to deform towards the population center, by following the deformation pathway simultaneously optimized within the graph. Our proposed method has been also compared with other state-of-the-art inter-group registration methods, where our method achieves better registration results in terms of registration accuracy and robustness. PMID:24443692

  2. Interactive initialization of 2D/3D rigid registration

    SciTech Connect

    Gong, Ren Hui; Güler, Özgür; Kürklüoglu, Mustafa; Lovejoy, John; Yaniv, Ziv

    2013-12-15

    Purpose: Registration is one of the key technical components in an image-guided navigation system. A large number of 2D/3D registration algorithms have been previously proposed, but have not been able to transition into clinical practice. The authors identify the primary reason for the lack of adoption with the prerequisite for a sufficiently accurate initial transformation, mean target registration error of about 10 mm or less. In this paper, the authors present two interactive initialization approaches that provide the desired accuracy for x-ray/MR and x-ray/CT registration in the operating room setting. Methods: The authors have developed two interactive registration methods based on visual alignment of a preoperative image, MR, or CT to intraoperative x-rays. In the first approach, the operator uses a gesture based interface to align a volume rendering of the preoperative image to multiple x-rays. The second approach uses a tracked tool available as part of a navigation system. Preoperatively, a virtual replica of the tool is positioned next to the anatomical structures visible in the volumetric data. Intraoperatively, the physical tool is positioned in a similar manner and subsequently used to align a volume rendering to the x-ray images using an augmented reality (AR) approach. Both methods were assessed using three publicly available reference data sets for 2D/3D registration evaluation. Results: In the authors' experiments, the authors show that for x-ray/MR registration, the gesture based method resulted in a mean target registration error (mTRE) of 9.3 ± 5.0 mm with an average interaction time of 146.3 ± 73.0 s, and the AR-based method had mTREs of 7.2 ± 3.2 mm with interaction times of 44 ± 32 s. For x-ray/CT registration, the gesture based method resulted in a mTRE of 7.4 ± 5.0 mm with an average interaction time of 132.1 ± 66.4 s, and the AR-based method had mTREs of 8.3 ± 5.0 mm with interaction times of 58 ± 52 s. Conclusions: Based on the

  3. The Role of Registration in Accurate Surgical Guidance

    PubMed Central

    Fitzpatrick, J. Michael

    2016-01-01

    Registration is presented as the central issue of surgical guidance. The focus is on the accuracy of approaches employed today, all of which use pre-operative images to guide surgery on rigid anatomy. The three most well established approaches to guidance—the stereotactic frame, point fiducials, and surface matching—are examined in detail, along with two new approaches based on microstereotactic frames. It is shown that each method relies on the registration of points in the image to corresponding points in the operating room, and therefore that the error patterns associated with point registration are similar for all of them. Three types of registration error—fiducial localization error (FLE), fiducial registration error (FRE), and target registration error (TRE) are highlighted, as well as two additional guidance errors—target localization error, and total targeting error, the latter of which is the overall error of the guidance system. Statistical relationships between TRE and FLE, between FRE and FLE, and among TRE, TLE and TTE are given. Finally some myths concerning fiducial registration are highlighted. PMID:20718266

  4. Three-dimensional warping registration of the pelvis and prostate

    NASA Astrophysics Data System (ADS)

    Fei, Baowei; Kemper, Corey; Wilson, David L.

    2002-05-01

    We are investigating interventional MRI guided radio- frequency (RF) thermal ablation for the minimally invasive treatment of prostate cancer. Among many potential applications of registration, we wish to compare registered MR images acquired before and immediately after RF ablation in order to determine whether a tumor is adequately treated. Warping registration is desired to correct for potential deformations of the pelvic region and movement of the prostate. We created a two-step, three-dimensional (3D) registration algorithm using mutual information and thin plate spline (TPS) warping for MR images. First, automatic rigid body registration was used to capture the global transformation. Second, local warping registration was applied. Interactively placed control points were automatically optimized by maximizing the mutual information of corresponding voxels in small volumes of interest and by using a 3D TPS to express the deformation throughout the image volume. Images were acquired from healthy volunteers in different conditions simulating potential applications. A variety of evaluation methods showed that warping consistently improved registration for volume pairs whenever patient position or condition was purposely changed between acquisitions. A TPS transformation based on 180 control points generated excellent warping throughout the pelvis following rigid body registration. The prostate centroid displacement for a typical volume pair was reduced from 3.4 mm to 0.6 mm when warping was added.

  5. High-accuracy registration of intraoperative CT imaging

    NASA Astrophysics Data System (ADS)

    Oentoro, A.; Ellis, R. E.

    2010-02-01

    Image-guided interventions using intraoperative 3D imaging can be less cumbersome than systems dependent on preoperative images, especially by needing neither potentially invasive image-to-patient registration nor a lengthy process of segmenting and generating a 3D surface model. In this study, a method for computer-assisted surgery using direct navigation on intraoperative imaging is presented. In this system the registration step of a navigated procedure was divided into two stages: preoperative calibration of images to a ceiling-mounted optical tracking system, and intraoperative tracking during acquisition of the 3D medical image volume. The preoperative stage used a custom-made multi-modal calibrator that could be optically tracked and also contained fiducial spheres for radiological detection; a robust registration algorithm was used to compensate for the very high false-detection rate that was due to the high physical density of the optical light-emitting diodes. Intraoperatively, a tracking device was attached to plastic bone models that were also instrumented with radio-opaque spheres; A calibrated pointer was used to contact the latter spheres as a validation of the registration. Experiments showed that the fiducial registration error of the preoperative calibration stage was approximately 0.1 mm. The target registration error in the validation stage was approximately 1.2 mm. This study suggests that direct registration, coupled with procedure-specific graphical rendering, is potentially a highly accurate means of performing image-guided interventions in a fast, simple manner.

  6. The role of registration in accurate surgical guidance.

    PubMed

    Fitzpatrick, J M

    2010-01-01

    Registration is presented as the central issue of surgical guidance. The focus is on the accuracy of approaches employed today, all of which use pre-operative images to guide surgery on rigid anatomy. The three most well-established approaches to guidance, namely the stereotactic frame, point fiducials, and surface matching, are examined in detail, together with two new approaches based on microstereotactic frames. It is shown that each method relies on the registration of points in the image to corresponding points in the operating room, and therefore that the error patterns associated with point registration are similar for all of them. Three types of registration error, namely fiducial localization error (FLE), fiducial registration error (FRE), and target registration error (TRE), are highlighted, as well as two additional guidance errors, namely target localization error and total targeting error, the latter of which is the overall error of the guidance system. Statistical relationships between TRE and FLE, between FRE and FLE, and between TRE, TLE, and TTE are given. Finally some myths concerning fiducial registration are highlighted. PMID:20718266

  7. PHARMACEUTICAL AND BIOMEDICAL APPLICATIONS OF AFFINITY CHROMATOGRAPHY: RECENT TRENDS AND DEVELOPMENTS

    PubMed Central

    Hage, David S.; Anguizola, Jeanethe A.; Bi, Cong; Li, Rong; Matsuda, Ryan; Papastavros, Efthimia; Pfaunmiller, Erika; Vargas, John; Zheng, Xiwei

    2012-01-01

    Affinity chromatography is a separation technique that has become increasingly important in work with biological samples and pharmaceutical agents. This method is based on the use of a biologically-related agent as a stationary phase to selectively retain analytes or to study biological interactions. This review discusses the basic principles behind affinity chromatography and examines recent developments that have occurred in the use of this method for biomedical and pharmaceutical analysis. Techniques based on traditional affinity supports are discussed, but an emphasis is placed on methods in which affinity columns are used as part of HPLC systems or in combination with other analytical methods. General formats for affinity chromatography that are considered include step elution schemes, weak affinity chromatography, affinity extraction and affinity depletion. Specific separation techniques that are examined include lectin affinity chromatography, boronate affinity chromatography, immunoaffinity chromatography, and immobilized metal ion affinity chromatography. Approaches for the study of biological interactions by affinity chromatography are also presented, such as the measurement of equilibrium constants, rate constants, or competition and displacement effects. In addition, related developments in the use of immobilized enzyme reactors, molecularly imprinted polymers, dye ligands and aptamers are briefly considered. PMID:22305083

  8. Protein affinity map of chemical space.

    PubMed

    Kauvar, L M; Villar, H O; Sportsman, J R; Higgins, D L; Schmidt, D E

    1998-09-11

    Affinity fingerprinting is a quantitative method for mapping chemical space based on binding preferences of compounds for a reference panel of proteins. An effective reference panel of <20 proteins can be empirically selected which shows differential interaction with nearly all compounds. By using this map to iteratively sample the chemical space, identification of active ligands from a library of 30,000 candidate compounds has been accomplished for a wide spectrum of specific protein targets. In each case, <200 compounds were directly assayed against the target. Further, analysis of the fingerprint database suggests a strategy for effective selection of affinity chromatography ligands and scaffolds for combinatorial chemistry. With such a system, the large numbers of potential therapeutic targets emerging from genome research can be categorized according to ligand binding properties, complementing sequence based classification. PMID:9792501

  9. Chasing polys: Interdisciplinary affinity and its connection to physics identity

    NASA Astrophysics Data System (ADS)

    Scott, Tyler D.

    This research is based on two motivations that merge by means of the frameworks of interdisciplinary affinity and physics identity. First, a goal of education is to develop interdisciplinary abilities in students' thinking and work. But an often ignored factor is students interests and beliefs about being interdisciplinary. Thus, this work develops and uses a framework called interdisciplinary affinity. It encompasses students interests in making connections across disciplines and their beliefs about their abilities to make those connections. The second motivation of this research is to better understand how to engage more students with physics. Physics identity describes how a student sees themselves in relation to physics. By understanding how physics identity is developed, researchers and educators can identify factors that increase interest and engagement in physics classrooms. Therefore, physics identity was used in conjunction with interdisciplinary affinity. Using a mixed methods approach, this research used quantitative data to identify the relationships interdisciplinary affinity has with physics identity and the physics classroom. These connections were explored in more detail using a case study of three students in a high school physics class. Results showed significant and positive relationships between interdisciplinary affinity and physics identity, including the individual interest and recognition components of identity. It also identified characteristics of physics classrooms that had a significant, positive relationship with interdisciplinary affinity. The qualitative case study highlighted the importance of student interest to the relationship between interdisciplinary affinity and physics identity. It also identified interest and mastery orientation as key to understanding the link between interdisciplinary affinity and the physics classroom. These results are a positive sign that by understanding interdisciplinary affinity and physics identity

  10. Satellite image registration based on the geometrical arrangement of objects

    NASA Astrophysics Data System (ADS)

    Bartl, Renate; Schneider, Werner

    1995-11-01

    The knowledge of the geometrical relationship between images is a prerequisite for registration. Assuming a conformal affine transformation, 4 transformation parameters have to be determined. This is done on the basis of the geometrical arrangement of characteristic objects extracted from images in a preprocessing step, for example a land use classification yielding forest, pond, or urban regions. The algorithm introduced establishes correspondence between (centers of gravity of) objects by building and matching so-called ANGLE CHAINS, a linear structure for representing a geometric (2D) arrangement. An example with satellite imagery illustrates the usefulness of the algorithm.

  11. Shearlet Features for Registration of Remotely Sensed Multitemporal Images

    NASA Technical Reports Server (NTRS)

    Murphy, James M.; Le Moigne, Jacqueline

    2015-01-01

    We investigate the role of anisotropic feature extraction methods for automatic image registration of remotely sensed multitemporal images. Building on the classical use of wavelets in image registration, we develop an algorithm based on shearlets, a mathematical generalization of wavelets that offers increased directional sensitivity. Initial experimental results on LANDSAT images are presented, which indicate superior performance of the shearlet algorithm when compared to classical wavelet algorithms.

  12. Image Registration: A Necessary Evil

    NASA Technical Reports Server (NTRS)

    Bell, James; McLachlan, Blair; Hermstad, Dexter; Trosin, Jeff; George, Michael W. (Technical Monitor)

    1995-01-01

    Registration of test and reference images is a key component of nearly all PSP data reduction techniques. This is done to ensure that a test image pixel viewing a particular point on the model is ratioed by the reference image pixel which views the same point. Typically registration is needed to account for model motion due to differing airloads when the wind-off and wind-on images are taken. Registration is also necessary when two cameras are used for simultaneous acquisition of data from a dual-frequency paint. This presentation will discuss the advantages and disadvantages of several different image registration techniques. In order to do so, it is necessary to propose both an accuracy requirement for image registration and a means for measuring the accuracy of a particular technique. High contrast regions in the unregistered images are most sensitive to registration errors, and it is proposed that these regions be used to establish the error limits for registration. Once this is done, the actual registration error can be determined by locating corresponding points on the test and reference images, and determining how well a particular registration technique matches them. An example of this procedure is shown for three transforms used to register images of a semispan model. Thirty control points were located on the model. A subset of the points were used to determine the coefficients of each registration transform, and the error with which each transform aligned the remaining points was determined. The results indicate the general superiority of a third-order polynomial over other candidate transforms, as well as showing how registration accuracy varies with number of control points. Finally, it is proposed that image registration may eventually be done away with completely. As more accurate image resection techniques and more detailed model surface grids become available, it will be possible to map raw image data onto the model surface accurately. Intensity

  13. An affinity selection-mass spectrometry method for the identification of small molecule ligands from self-encoded combinatorial libraries: Discovery of a novel antagonist of E. coli dihydrofolate reductase

    NASA Astrophysics Data System (ADS)

    Annis, D. Allen; Athanasopoulos, John; Curran, Patrick J.; Felsch, Jason S.; Kalghatgi, Krishna; Lee, William H.; Nash, Huw M.; Orminati, Jean-Paul A.; Rosner, Kristin E.; Shipps, Gerald W., Jr.; Thaddupathy, G. R. A.; Tyler, Andrew N.; Vilenchik, Lev; Wagner, Carston R.; Wintner, Edward A.

    2004-11-01

    The NeoGenesis Automated Ligand Identification System (ALIS), an affinity selection-mass spectrometry (AS-MS) process consisting of a rapid size-exclusion chromatography stage integrated with reverse-phase chromatography, electrospray mass spectrometry, and novel data searching algorithms, was used to screen mass-encoded, 2500-member combinatorial libraries, leading to the discovery of a novel, bioactive ligand for the anti-infective target Escherichia coli dihydrofolate reductase (DHFR). Synthesis of the mass-encoded, ligand-containing library, discussion of the deconvolution process for verifying the structure of the ligand through independent synthesis and screening in a small mixture (sub-library) format, and ALIS-MS/MS techniques to assign its regioisomeric connectivity are presented. ALIS-based competition experiments between the newly discovered ligand and other, known DHFR ligands, and biological activity assessments with stereo- and regioisomers of the hit compound confirm its DHFR-specific biological activity. The method described requires no foreknowledge of the structure or biochemistry of the protein target, consumes less than 1 [mu]g protein to screen >2500 compounds in a single experiment, and enables screening of >250,000 compounds per system per day. These advantages highlight the potential of the ALIS method for drug discovery against genomic targets with unknown biological function, as well as validated targets for which traditional discovery efforts have failed.

  14. Affinity+: Semi-Structured Brainstorming on Large Displays

    SciTech Connect

    Burtner, Edwin R.; May, Richard A.; Scarberry, Randall E.; LaMothe, Ryan R.; Endert, Alexander

    2013-04-27

    Affinity diagraming is a powerful method for encouraging and capturing lateral thinking in a group environment. The Affinity+ Concept was designed to improve the collaborative brainstorm process through the use of large display surfaces in conjunction with mobile devices like smart phones and tablets. The system works by capturing the ideas digitally and allowing users to sort and group them on a large touch screen manually. Additionally, Affinity+ incorporates theme detection, topic clustering, and other processing algorithms that help bring structured analytic techniques to the process without requiring explicit leadership roles and other overhead typically involved in these activities.

  15. Comparative Study of Two Automatic Registration Algorithms

    NASA Astrophysics Data System (ADS)

    Grant, D.; Bethel, J.; Crawford, M.

    2013-10-01

    The Iterative Closest Point (ICP) algorithm is prevalent for the automatic fine registration of overlapping pairs of terrestrial laser scanning (TLS) data. This method along with its vast number of variants, obtains the least squares parameters that are necessary to align the TLS data by minimizing some distance metric between the scans. The ICP algorithm uses a "model-data" concept in which the scans obtain differential treatment in the registration process depending on whether they were assigned to be the "model" or "data". For each of the "data" points, corresponding points from the "model" are sought. Another concept of "symmetric correspondence" was proposed in the Point-to-Plane (P2P) algorithm, where both scans are treated equally in the registration process. The P2P method establishes correspondences on both scans and minimizes the point-to-plane distances between the scans by simultaneously considering the stochastic properties of both scans. This paper studies both the ICP and P2P algorithms in terms of their consistency in registration parameters for pairs of TLS data. The question being investigated in this paper is, should scan A be registered to scan B, will the parameters be the same if scan B were registered to scan A? Experiments were conducted with eight pairs of real TLS data which were registered by the two algorithms in the forward (scan A to scan B) and backward (scan B to scan A) modes and the results were compared. The P2P algorithm was found to be more consistent than the ICP algorithm. The differences in registration accuracy between the forward and backward modes were negligible when using the P2P algorithm (mean difference of 0.03 mm). However, the ICP had a mean difference of 4.26 mm. Each scan was also transformed by the forward and backward parameters of the two algorithms and the misclosure computed. The mean misclosure for the P2P algorithm was 0.80 mm while that for the ICP algorithm was 5.39 mm. The conclusion from this study is

  16. Overlay improvement by exposure map based mask registration optimization

    NASA Astrophysics Data System (ADS)

    Shi, Irene; Guo, Eric; Chen, Ming; Lu, Max; Li, Gordon; Li, Rivan; Tian, Eric

    2015-03-01

    Along with the increased miniaturization of semiconductor electronic devices, the design rules of advanced semiconductor devices shrink dramatically. [1] One of the main challenges of lithography step is the layer-to-layer overlay control. Furthermore, DPT (Double Patterning Technology) has been adapted for the advanced technology node like 28nm and 14nm, corresponding overlay budget becomes even tighter. [2][3] After the in-die mask registration (pattern placement) measurement is introduced, with the model analysis of a KLA SOV (sources of variation) tool, it's observed that registration difference between masks is a significant error source of wafer layer-to-layer overlay at 28nm process. [4][5] Mask registration optimization would highly improve wafer overlay performance accordingly. It was reported that a laser based registration control (RegC) process could be applied after the pattern generation or after pellicle mounting and allowed fine tuning of the mask registration. [6] In this paper we propose a novel method of mask registration correction, which can be applied before mask writing based on mask exposure map, considering the factors of mask chip layout, writing sequence, and pattern density distribution. Our experiment data show if pattern density on the mask keeps at a low level, in-die mask registration residue error in 3sigma could be always under 5nm whatever blank type and related writer POSCOR (position correction) file was applied; it proves random error induced by material or equipment would occupy relatively fixed error budget as an error source of mask registration. On the real production, comparing the mask registration difference through critical production layers, it could be revealed that registration residue error of line space layers with higher pattern density is always much larger than the one of contact hole layers with lower pattern density. Additionally, the mask registration difference between layers with similar pattern density

  17. Affinity Purification of Antibodies.

    PubMed

    Hnasko, Robert M; McGarvey, Jeffery A

    2015-01-01

    Antibodies are provided in a variety of formats that include antiserum, hybridoma culture supernatant, or ascites. They can all be used successfully in crude form for the detection of target antigens by immunoassay. However, it is advantageous to use purified antibody in defined quantity to facilitate assay reproducibility, economy, and reduced interference of nonspecific components as well as improved storage, stability, and bio-conjugation. Although not always necessary, the relative simplicity of antibody purification using commercially available protein-A, protein-G, or protein-L resins with basic chromatographic principles warrants purification when antibody source material is available in sufficient quantity. Here, we define three simple methods using immobilized (1) protein-A, (2) protein-G, and (3) protein-L agarose beads to yield highly purified antibody. PMID:26160561

  18. MR to CT registration of brains using image synthesis

    NASA Astrophysics Data System (ADS)

    Roy, Snehashis; Carass, Aaron; Jog, Amod; Prince, Jerry L.; Lee, Junghoon

    2014-03-01

    Computed tomography (CT) is the preferred imaging modality for patient dose calculation for radiation therapy. Magnetic resonance (MR) imaging (MRI) is used along with CT to identify brain structures due to its superior soft tissue contrast. Registration of MR and CT is necessary for accurate delineation of the tumor and other structures, and is critical in radiotherapy planning. Mutual information (MI) or its variants are typically used as a similarity metric to register MRI to CT. However, unlike CT, MRI intensity does not have an accepted calibrated intensity scale. Therefore, MI-based MR-CT registration may vary from scan to scan as MI depends on the joint histogram of the images. In this paper, we propose a fully automatic framework for MR-CT registration by synthesizing a synthetic CT image from MRI using a co-registered pair of MR and CT images as an atlas. Patches of the subject MRI are matched to the atlas and the synthetic CT patches are estimated in a probabilistic framework. The synthetic CT is registered to the original CT using a deformable registration and the computed deformation is applied to the MRI. In contrast to most existing methods, we do not need any manual intervention such as picking landmarks or regions of interests. The proposed method was validated on ten brain cancer patient cases, showing 25% improvement in MI and correlation between MR and CT images after registration compared to state-of-the-art registration methods.

  19. Skeleton Graph Matching vs. Maximum Weight Cliques aorta registration techniques.

    PubMed

    Czajkowska, Joanna; Feinen, C; Grzegorzek, M; Raspe, M; Wickenhöfer, R

    2015-12-01

    Vascular diseases are one of the most challenging health problems in developed countries. Past as well as ongoing research activities often focus on efficient, robust and fast aorta segmentation, and registration techniques. According to this needs our study targets an abdominal aorta registration method. The investigated algorithms make it possible to efficiently segment and register abdominal aorta in pre- and post-operative Computed Tomography (CT) data. In more detail, a registration technique using the Path Similarity Skeleton Graph Matching (PSSGM), as well as Maximum Weight Cliques (MWCs) are employed to realise the matching based on Computed Tomography data. The presented approaches make it possible to match characteristic voxels belonging to the aorta from different Computed Tomography (CT) series. It is particularly useful in the assessment of the abdominal aortic aneurysm treatment by visualising the correspondence between the pre- and post-operative CT data. The registration results have been tested on the database of 18 contrast-enhanced CT series, where the cross-registration analysis has been performed producing 153 matching examples. All the registration results achieved with our system have been verified by an expert. The carried out analysis has highlighted the advantage of the MWCs technique over the PSSGM method. The verification phase proves the efficiency of the MWCs approach and encourages to further develop this methods. PMID:26099640

  20. 7 CFR 800.34 - Registration fee.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Registration fee. 800.34 Section 800.34 Agriculture... ADMINISTRATION (FEDERAL GRAIN INSPECTION SERVICE), DEPARTMENT OF AGRICULTURE GENERAL REGULATIONS Registration § 800.34 Registration fee. An applicant shall submit the registration fee prescribed in § 800.71...

  1. 9 CFR 381.179 - Registration.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 false Registration. 381.179 Section 381.179... CERTIFICATION POULTRY PRODUCTS INSPECTION REGULATIONS Records, Registration, and Reports § 381.179 Registration... effective date. All information submitted shall be current and correct. The registration form shall...

  2. 7 CFR 800.34 - Registration fee.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 7 2011-01-01 2011-01-01 false Registration fee. 800.34 Section 800.34 Agriculture... ADMINISTRATION (FEDERAL GRAIN INSPECTION SERVICE), DEPARTMENT OF AGRICULTURE GENERAL REGULATIONS Registration § 800.34 Registration fee. An applicant shall submit the registration fee prescribed in § 800.71...

  3. 44 CFR 206.112 - Registration period.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 44 Emergency Management and Assistance 1 2011-10-01 2011-10-01 false Registration period. 206.112... Households § 206.112 Registration period. (a) Initial period. The standard FEMA registration period is 60...) Extension of the registration period. The regional administrator or his/her designee may extend...

  4. 27 CFR 17.21 - Registration.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Registration. 17.21... PRODUCTS Registration § 17.21 Registration. Every person claiming drawback under this part must register annually as a nonbeverage domestic drawback claimant. Registration will be accomplished when the...

  5. 32 CFR 634.19 - Registration policy.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 4 2011-07-01 2011-07-01 false Registration policy. 634.19 Section 634.19... CRIMINAL INVESTIGATIONS MOTOR VEHICLE TRAFFIC SUPERVISION Motor Vehicle Registration § 634.19 Registration... registration of off-road vehicles and bicycles under a separate local system. (c) Commanders can grant...

  6. 27 CFR 17.21 - Registration.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Registration. 17.21... PRODUCTS Registration § 17.21 Registration. Every person claiming drawback under this part must register annually as a nonbeverage domestic drawback claimant. Registration will be accomplished when the...

  7. 32 CFR 634.19 - Registration policy.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 4 2010-07-01 2010-07-01 true Registration policy. 634.19 Section 634.19... CRIMINAL INVESTIGATIONS MOTOR VEHICLE TRAFFIC SUPERVISION Motor Vehicle Registration § 634.19 Registration... registration of off-road vehicles and bicycles under a separate local system. (c) Commanders can grant...

  8. 28 CFR 5.200 - Registration.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Registration. 5.200 Section 5.200 Judicial Administration DEPARTMENT OF JUSTICE ADMINISTRATION AND ENFORCEMENT OF FOREIGN AGENTS REGISTRATION ACT OF 1938, AS AMENDED § 5.200 Registration. (a) Registration under the Act is accomplished by...

  9. 28 CFR 5.200 - Registration.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 28 Judicial Administration 1 2011-07-01 2011-07-01 false Registration. 5.200 Section 5.200 Judicial Administration DEPARTMENT OF JUSTICE ADMINISTRATION AND ENFORCEMENT OF FOREIGN AGENTS REGISTRATION ACT OF 1938, AS AMENDED § 5.200 Registration. (a) Registration under the Act is accomplished by...

  10. 9 CFR 381.179 - Registration.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Registration. 381.179 Section 381.179... CERTIFICATION POULTRY PRODUCTS INSPECTION REGULATIONS Records, Registration, and Reports § 381.179 Registration... effective date. All information submitted shall be current and correct. The registration form shall...

  11. 40 CFR 79.13 - Registration.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... OF FUELS AND FUEL ADDITIVES Fuel Registration Procedures § 79.13 Registration. (a) If the Administrator determines that a manufacturer has submitted an application for registration of a designated fuel... the fuel and notify the fuel manufacturer of such registration. (b) The Administrator shall maintain...

  12. 40 CFR 79.13 - Registration.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... OF FUELS AND FUEL ADDITIVES Fuel Registration Procedures § 79.13 Registration. (a) If the Administrator determines that a manufacturer has submitted an application for registration of a designated fuel... the fuel and notify the fuel manufacturer of such registration. (b) The Administrator shall maintain...

  13. Phosphopeptide Enrichment by Immobilized Metal Affinity Chromatography.

    PubMed

    Thingholm, Tine E; Larsen, Martin R

    2016-01-01

    Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively charged metal ions such as Fe(3+), Ga(3+), Al(3+), Zr(4+), and Ti(4+) has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from nonspecific binding of non-phosphorylated peptides. This problem is mainly caused by highly acidic peptides that also share high binding affinity towards these metal ions. By lowering the pH of the loading buffer nonspecific binding can be reduced significantly, however with the risk of reducing specific binding capacity. After binding, the enriched phosphopeptides are released from the metal ions using alkaline buffers of pH 10-11, EDTA, or phosphate-containing buffers. Here we describe a protocol for IMAC using Fe(3+) for phosphopeptide enrichment. The principles are illustrated on a semi-complex peptide mixture. PMID:26584922

  14. Sensor registration using airlanes: maximum likelihood solution

    NASA Astrophysics Data System (ADS)

    Ong, Hwa-Tung

    2004-01-01

    In this contribution, the maximum likelihood estimation of sensor registration parameters, such as range, azimuth and elevation biases in radar measurements, using airlane information is proposed and studied. The motivation for using airlane information for sensor registration is that it is freely available as a source of reference and it provides an alternative to conventional techniques that rely on synchronised and correctly associated measurements from two or more sensors. In the paper, the problem is first formulated in terms of a measurement model that is a nonlinear function of the unknown target state and sensor parameters, plus sensor noise. A probabilistic model of the target state is developed based on airlane information. The maximum likelihood and also maximum a posteriori solutions are given. The Cramer-Rao lower bound is derived and simulation results are presented for the case of estimating the biases in radar range, azimuth and elevation measurements. The accuracy of the proposed method is compared against the Cramer-Rao lower bound and that of an existing two-sensor alignment method. It is concluded that sensor registration using airlane information is a feasible alternative to existing techniques.

  15. Sensor registration using airlanes: maximum likelihood solution

    NASA Astrophysics Data System (ADS)

    Ong, Hwa-Tung

    2003-12-01

    In this contribution, the maximum likelihood estimation of sensor registration parameters, such as range, azimuth and elevation biases in radar measurements, using airlane information is proposed and studied. The motivation for using airlane information for sensor registration is that it is freely available as a source of reference and it provides an alternative to conventional techniques that rely on synchronised and correctly associated measurements from two or more sensors. In the paper, the problem is first formulated in terms of a measurement model that is a nonlinear function of the unknown target state and sensor parameters, plus sensor noise. A probabilistic model of the target state is developed based on airlane information. The maximum likelihood and also maximum a posteriori solutions are given. The Cramer-Rao lower bound is derived and simulation results are presented for the case of estimating the biases in radar range, azimuth and elevation measurements. The accuracy of the proposed method is compared against the Cramer-Rao lower bound and that of an existing two-sensor alignment method. It is concluded that sensor registration using airlane information is a feasible alternative to existing techniques.

  16. Hierarchical model-based interferometric synthetic aperture radar image registration

    NASA Astrophysics Data System (ADS)

    Wang, Yang; Huang, Haifeng; Dong, Zhen; Wu, Manqing

    2014-01-01

    With the rapid development of spaceborne interferometric synthetic aperture radar technology, classical image registration methods are incompetent for high-efficiency and high-accuracy masses of real data processing. Based on this fact, we propose a new method. This method consists of two steps: coarse registration that is realized by cross-correlation algorithm and fine registration that is realized by hierarchical model-based algorithm. Hierarchical model-based algorithm is a high-efficiency optimization algorithm. The key features of this algorithm are a global model that constrains the overall structure of the motion estimated, a local model that is used in the estimation process, and a coarse-to-fine refinement strategy. Experimental results from different kinds of simulated and real data have confirmed that the proposed method is very fast and has high accuracy. Comparing with a conventional cross-correlation method, the proposed method provides markedly improved performance.

  17. Affine Contractions on the Plane

    ERIC Educational Resources Information Center

    Celik, D.; Ozdemir, Y.; Ureyen, M.

    2007-01-01

    Contractions play a considerable role in the theory of fractals. However, it is not easy to find contractions which are not similitudes. In this study, it is shown by counter examples that an affine transformation of the plane carrying a given triangle onto another triangle may not be a contraction even if it contracts edges, heights or medians.…

  18. Quantifying Affinity among Chinese Dialects.

    ERIC Educational Resources Information Center

    Cheng, Chin-Chuan

    A study of the relationships between Chinese dialects based on a quantitative measure of dialect affinity is summarized. First, tone values in all the dialect localities available in the early 1970s were used to calculate the dialectal differences in terms of tone height with respect to the "yin and yang" split. In the late 1970s, calculations of…

  19. Aptamer-modified magnetic beads in affinity separation of proteins.

    PubMed

    Zhu, Guohong; Walter, Johanna-Gabriela

    2015-01-01

    Aptamers are valuable alternative ligands for affinity separations. Here, we describe the aptamer-based affinity separation of His-tagged proteins using an aptamer directed against the His-tag. The immobilization of the aptamer to magnetic beads is described as well as the aptamer-based purification and proper methods for the characterization of the process. Moreover, indications for the transfer of the process to other aptamers are given. PMID:25749947

  20. Visible and infrared image registration based on visual salient features

    NASA Astrophysics Data System (ADS)

    Wu, Feihong; Wang, Bingjian; Yi, Xiang; Li, Min; Hao, Jingya; Qin, Hanlin; Zhou, Huixin

    2015-09-01

    In order to improve the precision of visible and infrared (VIS/IR) image registration, an image registration method based on visual salient (VS) features is presented. First, a VS feature detector based on the modified visual attention model is presented to extract VS points. Because the iterative, within-feature competition method used in visual attention models is time consuming, an alternative fast visual salient (FVS) feature detector is proposed to make VS features more efficient. Then, a descriptor-rearranging (DR) strategy is adopted to describe feature points. This strategy combines information of both IR image and its negative image to overcome the contrast reverse problem between VIS and IR images, making it easier to find the corresponding points on VIS/IR images. Experiments show that both VS and FVS detectors have higher repeatability scores than scale invariant feature transform in the cases of blurring, brightness change, JPEG compression, noise, and viewpoint, except big scale change. The combination of VS detector and DR registration strategy can achieve precise image registration, but it is time-consuming. The combination of FVS detector and DR registration strategy can also reach a good registration of VIS/IR images but in a shorter time.

  1. Fast 3D fluid registration of brain magnetic resonance images

    NASA Astrophysics Data System (ADS)

    Leporé, Natasha; Chou, Yi-Yu; Lopez, Oscar L.; Aizenstein, Howard J.; Becker, James T.; Toga, Arthur W.; Thompson, Paul M.

    2008-03-01

    Fluid registration is widely used in medical imaging to track anatomical changes, to correct image distortions, and to integrate multi-modality data. Fluid mappings guarantee that the template image deforms smoothly into the target, without tearing or folding, even when large deformations are required for accurate matching. Here we implemented an intensity-based fluid registration algorithm, accelerated by using a filter designed by Bro-Nielsen and Gramkow. We validated the algorithm on 2D and 3D geometric phantoms using the mean square difference between the final registered image and target as a measure of the accuracy of the registration. In tests on phantom images with different levels of overlap, varying amounts of Gaussian noise, and different intensity gradients, the fluid method outperformed a more commonly used elastic registration method, both in terms of accuracy and in avoiding topological errors during deformation. We also studied the effect of varying the viscosity coefficients in the viscous fluid equation, to optimize registration accuracy. Finally, we applied the fluid registration algorithm to a dataset of 2D binary corpus callosum images and 3D volumetric brain MRIs from 14 healthy individuals to assess its accuracy and robustness.

  2. Registration algorithm of point clouds based on multiscale normal features

    NASA Astrophysics Data System (ADS)

    Lu, Jun; Peng, Zhongtao; Su, Hang; Xia, GuiHua

    2015-01-01

    The point cloud registration technology for obtaining a three-dimensional digital model is widely applied in many areas. To improve the accuracy and speed of point cloud registration, a registration method based on multiscale normal vectors is proposed. The proposed registration method mainly includes three parts: the selection of key points, the calculation of feature descriptors, and the determining and optimization of correspondences. First, key points are selected from the point cloud based on the changes of magnitude of multiscale curvatures obtained by using principal components analysis. Then the feature descriptor of each key point is proposed, which consists of 21 elements based on multiscale normal vectors and curvatures. The correspondences in a pair of two point clouds are determined according to the descriptor's similarity of key points in the source point cloud and target point cloud. Correspondences are optimized by using a random sampling consistency algorithm and clustering technology. Finally, singular value decomposition is applied to optimized correspondences so that the rigid transformation matrix between two point clouds is obtained. Experimental results show that the proposed point cloud registration algorithm has a faster calculation speed, higher registration accuracy, and better antinoise performance.

  3. Globally consistent registration of terrestrial laser scans via graph optimization

    NASA Astrophysics Data System (ADS)

    Theiler, Pascal Willy; Wegner, Jan Dirk; Schindler, Konrad

    2015-11-01

    In this paper we present a framework for the automatic registration of multiple terrestrial laser scans. The proposed method can handle arbitrary point clouds with reasonable pairwise overlap, without knowledge about their initial orientation and without the need for artificial markers or other specific objects. The framework is divided into a coarse and a fine registration part, which each start with pairwise registration and then enforce consistent global alignment across all scans. While we put forward a complete, functional registration system, the novel cont