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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. 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.

  3. Improving the convergence rate in affine registration of PET and SPECT brain images using histogram equalization.

    PubMed

    Salas-Gonzalez, D; Górriz, J M; Ramírez, J; Padilla, P; Illán, I A

    2013-01-01

    A procedure to improve the convergence rate for affine registration methods of medical brain images when the images differ greatly from the template is presented. The methodology is based on a histogram matching of the source images with respect to the reference brain template before proceeding with the affine registration. The preprocessed source brain images are spatially normalized to a template using a general affine model with 12 parameters. A sum of squared differences between the source images and the template is considered as objective function, and a Gauss-Newton optimization algorithm is used to find the minimum of the cost function. Using histogram equalization as a preprocessing step improves the convergence rate in the affine registration algorithm of brain images as we show in this work using SPECT and PET brain images.

  4. [Affine transformation-based automatic registration for peripheral digital subtraction angiography (DSA)].

    PubMed

    Kong, Gang; Dai, Dao-Qing; Zou, Lu-Min

    2008-07-01

    In order to remove the artifacts of peripheral digital subtraction angiography (DSA), an affine transformation-based automatic image registration algorithm is introduced here. The whole process is described as follows: First, rectangle feature templates are constructed with their centers of the extracted Harris corners in the mask, and motion vectors of the central feature points are estimated using template matching technology with the similarity measure of maximum histogram energy. And then the optimal parameters of the affine transformation are calculated with the matrix singular value decomposition (SVD) method. Finally, bilinear intensity interpolation is taken to the mask according to the specific affine transformation. More than 30 peripheral DSA registrations are performed with the presented algorithm, and as the result, moving artifacts of the images are removed with sub-pixel precision, and the time consumption is less enough to satisfy the clinical requirements. Experimental results show the efficiency and robustness of the algorithm.

  5. [A coarse-to-fine registration method for satellite infrared image and visual image].

    PubMed

    Hu, Yong-Li; Wang, Liang; Liu, Rong; Zhang, Li; Duan, Fu-Qing

    2013-11-01

    In the present paper, in order to resolve the registration of the multi-mode satellite images with different signal properties and features, a two-phase coarse-to-fine registration method is presented and is applied to the registration of satellite infrared images and visual images. In the coarse registration phase of this method, the edge of infrared and visual images is firstly detected. Then the Fourier-Mellin transform is adopted to process the edge images. Finally, the affine transformation parameters of the registration are computed rapidly by the transformation relation between the registering images in frequency domain. In the fine registration phase of the proposed method, the feature points of infrared and visual images are firstly detected by Harris operator. Then the matched feature points of infrared and visual images are determined by the cross-correlation similarity of their local neighborhoods. The fine registration is finally realized according to the spatial correspondent relation of the matched feature points in infrared and visual images. The proposed coarse-to-fine registration method derives both the advantages of two methods, the high efficiency of Fourier-Mellin transform based registration method and the accuracy of Harris operator based registration method, which is considered the novelty and merit of the proposed method. To evaluate the performance of the proposed registration method, the coarse-to-fine registration method is implemented on the infrared and visual images captured by the FY-2D meteorological satellite. The experimental results show that the presented registration method is robust and has acceptable registration accuracy.

  6. 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

  7. Estimation of two-dimensional affine transformations through polar curve matching and its application to image mosaicking and remote-sensing data registration.

    PubMed

    Lucchese, Luca; Leorin, Simone; Cortelazzo, Guido M

    2006-10-01

    This paper presents a new and effective method for estimating two-dimensional affine transformations and its application to image registration. The method is based on matching polar curves obtained from the radial projections of the image energies, defined as the squared magnitudes of their Fourier transforms. Such matching is formulated as a simple minimization problem whose optimal solution is found with the Levenberg-Marquardt algorithm. The analysis of affine transformations in the frequency domain exploits the well-known property whereby the translational displacement in this domain can be factored out and separately estimated through phase correlation after the four remaining degrees of freedom of the affine warping have been determined. Another important contribution of this paper, emphasized through one example of image mosaicking and one example of remote sensing image registration, consists in showing that affine motion can be accurately estimated by applying our algorithm to the shapes of macrofeatures extracted from the images to register. The excellent performance of the algorithm is also shown through a synthetic example of motion estimation and its comparison with another standard registration technique.

  8. 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.

  9. 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.

  10. Complexity and accuracy of image registration methods in SPECT-guided radiation therapy

    NASA Astrophysics Data System (ADS)

    Yin, L. S.; Tang, L.; Hamarneh, G.; Gill, B.; Celler, A.; Shcherbinin, S.; Fua, T. F.; Thompson, A.; Liu, M.; Duzenli, C.; Sheehan, F.; Moiseenko, V.

    2010-01-01

    The use of functional imaging in radiotherapy treatment (RT) planning requires accurate co-registration of functional imaging scans to CT scans. We evaluated six methods of image registration for use in SPECT-guided radiotherapy treatment planning. Methods varied in complexity from 3D affine transform based on control points to diffeomorphic demons and level set non-rigid registration. Ten lung cancer patients underwent perfusion SPECT-scans prior to their radiotherapy. CT images from a hybrid SPECT/CT scanner were registered to a planning CT, and then the same transformation was applied to the SPECT images. According to registration evaluation measures computed based on the intensity difference between the registered CT images or based on target registration error, non-rigid registrations provided a higher degree of accuracy than rigid methods. However, due to the irregularities in some of the obtained deformation fields, warping the SPECT using these fields may result in unacceptable changes to the SPECT intensity distribution that would preclude use in RT planning. Moreover, the differences between intensity histograms in the original and registered SPECT image sets were the largest for diffeomorphic demons and level set methods. In conclusion, the use of intensity-based validation measures alone is not sufficient for SPECT/CT registration for RTTP. It was also found that the proper evaluation of image registration requires the use of several accuracy metrics.

  11. 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.

  12. 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

  13. An automatic registration method based on runway detection

    NASA Astrophysics Data System (ADS)

    Zhang, Xiuqiong; Yu, Li; Huang, Guo

    2014-04-01

    Runway is seen distinctly that is a crucial condition in the process of approaching and landing. One of the enhanced vision methods is image fusion method between the infrared and visible images in EVS (Enhanced Vision System). The image registration plays a very important role in image fusion. So, an automatic image registration method is proposed based on the accurate runway detection. Firstly, runway is detected using DWT (discrete wavelets transform) from the infrared and visible images respectively. Then, a fitting triangle is constructed according to the edges of runway. The corresponding feature points extracted from the middle points of edges and the centroid of triangle are used to compute the transform parameters. The results of registration are more accurate and efficient than those of registration based on mutual information. This method is robust and has less computation which can be applied to real-time system.

  14. Dense Stereo Matching Method Based on Local Affine Model.

    PubMed

    Li, Jie; Shi, Wenxuan; Deng, Dexiang; Jia, Wenyan; Sun, Mingui

    2013-07-01

    A new method for constructing an accurate disparity space image and performing an efficient cost aggregation in stereo matching based on local affine model is proposed in this paper. The key algorithm includes a new self-adapting dissimilarity measurement used for calculating the matching cost and a local affine model used in cost aggregation stage. Different from the traditional region-based methods, which try to change the matching window size or to calculate an adaptive weight to do the aggregation, the proposed method focuses on obtaining the efficient and accurate local affine model to aggregate the cost volume while preserving the disparity discontinuity. Moreover, the local affine model can be extended to the color space. Experimental results demonstrate that the proposed method is able to provide subpixel precision disparity maps compared with some state-of-the-art stereo matching methods. PMID:24163727

  15. 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%.

  16. Automatic registration method for mobile LiDAR data

    NASA Astrophysics Data System (ADS)

    Wang, Ruisheng; Ferrie, Frank P.

    2015-01-01

    We present an automatic mutual information (MI) registration method for mobile LiDAR and panoramas collected from a driving vehicle. The suitability of MI for registration of aerial LiDAR and aerial oblique images has been demonstrated under an assumption that minimization of joint entropy (JE) is a sufficient approximation of maximization of MI. We show that this assumption is invalid for the ground-level data. The entropy of a LiDAR image cannot be regarded as approximately constant for small perturbations. Instead of minimizing the JE, we directly maximize MI to estimate corrections of camera poses. Our method automatically registers mobile LiDAR with spherical panoramas over an approximate 4-km drive, and is the first example we are aware of that tests MI registration in a large-scale context.

  17. 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.

  18. 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.

  19. A new patient registration method for intensive care department management.

    PubMed

    Van Aken, P; Bossaert, L; Gilot, C; Tielemans, L

    1987-01-01

    A new method to describe intensive care department performance is presented. The method is a complication of available administrative and medical data, completed with a severity of illness measure (Acute Physiology And Chronic Health Evaluation, APACHE) and the registration of nursing care intensity. The development of this latter patient stratification system (Intensive Care Activity Score, INCAS) is described. The performance of the method is demonstrated by a study of 200 consecutive admissions.

  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. 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.

  2. Articulated registration: elastic registration based on a wire-model

    NASA Astrophysics Data System (ADS)

    Martin-Fernandez, Miguel A.; Munyoz-Moreno, Emma; Martin-Fernandez, Marcos; Alberola-Lopez, Carlos

    2005-04-01

    In this paper we propose a new method of elastic registration of anatomical structures that bears an inner skeleton, such as the knee, hand or spine. Such a method has to deal with great degrees of variability, specially for the case of inter-subject registration; but even for the intra-subject case the degree of variability of images will be large since the structures we bear in mind are articulated. Rigid registration methods are clearly inappropriate for this problem, and well-known elastic methods do not usually incorporate the restriction of maintaining long skeletal structures straight. A new method is therefore needed to deal with such a situation; we call this new method "articulated registration". The inner bone skeleton is modeled with a wire model, where wires are drawn by connecting landmarks located in the main joints of the skeletal structure to be registered (long bones). The main feature of our registration method is that within the bone axis (specifically, where the wires are) an exact registration is guaranteed, while for the remaining image points an elastic registration is carried out based on a distance transform (with respect to the model wires); this causes the registration on long bones to be affine to all practical purposes, while the registration of soft tissue -- far from the bones -- is elastic. As a proof-of-concept of this method we describe the registration of hands on radiographs.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.

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

    DOEpatents

    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.

  17. 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

  18. Registration method for infrared images under conditions of fixed-pattern noise

    NASA Astrophysics Data System (ADS)

    Zuo, Chao; Chen, Qian; Gu, Guohua; Sui, Xiubao

    2012-05-01

    This paper proposes a new registration method for infrared images under conditions of fixed-pattern noise (FPN). Conventional registration techniques are susceptible to FPN and it is therefore very desirable to have a registration algorithm that is tolerant to FPN. For this purpose, we utilize the difference of the cross-power spectrum of two discrete shifted images to suppress the noise power spectrum while the shifts information is well preserved. In particular, we show that the phase of the cross-power spectrum difference is a periodic two-dimensional binary stripe signal with the exact shifts determined to subpixel accuracy by the number of periods of the phase difference along each frequency axis. Robust estimates of shifts can be obtained by transforming its discontinuities to Hough domain. Experimental results show that the proposed method exhibits robust and accurate registration performance even for the noisy images that could not be handled by conventional registration algorithms. We have also incorporated this technique to a registration-based nonuniformity correction (NUC) framework, indicating that our registration technique is able to estimate motion parameters reliably, leading to satisfactory NUC result.

  19. Fully automatic hybrid registration method based on point feature detection without user intervention

    NASA Astrophysics Data System (ADS)

    Koo, Bang-Bon; Lee, Jong-Min; Kim, June-Sic; Kim, In-Young; Kwon, Jun-Soo; Kim, Sun I.

    2006-03-01

    In earlier work (KIM, J.S, MBEC, 2003), we demonstrated the registration method with a non-linear transformation using intensity similarity and feature similarity. Although the former approach showed good match in global shape of brain and feature-defined region, method contains user interventions for defining appropriate and sufficient number features. While manual delineating the region of interests for sufficient number of feature is a very time-consuming and can provide intra-, inter-rater variability, we proposed fully automatic hybrid registration via automatic feature defining method. Automatic feature definition was performed on the cortical surface from CLASP (KIM, J.S, Neuroimage, 2005) with using cortical surface matching algorithm (Robbins, S., MIA, 2004) and then applied to hybrid registration. The object of this work is to develop fully automated hybrid registration method which reveals enhanced performance in comparison to previous automated registration methods. In the result, our proposed scheme showed efficient performance from maintaining the strong points of hybrid registration without any user intervention.

  20. A hybrid registration-based method for whole-body micro-CT mice images.

    PubMed

    Qu, Xiaochao; Gao, Xueyuan; Xu, Xianhui; Zhu, Shouping; Liang, Jimin

    2016-07-01

    The widespread use of whole-body small animal in vivo imaging in preclinical research has proposed the new demands on imaging processing and analysis. Micro-CT provides detailed anatomical structural information for continuous detection and different individual comparison, but the body deformation happened during different data acquisition needs sophisticated registration. In this paper, we propose a hybrid method for registering micro-CT mice images, which combines the strengths of point-based and intensity-based registration methods. Point-based non-rigid method using thin-plate spline robust point matching algorithm is utilized to acquire a coarse registration. And then intensity-based non-rigid method using normalized mutual information, Halton sampling and adaptive stochastic gradient descent optimization is used to acquire precise registration. Two accuracy metrics, Dice coefficient and average surface distance are used to do the quantitative evaluation. With the intra- and intersubject micro-CT mice images registration assessment, the hybrid method has been proven capable of excellent performance on micro-CT mice images registration.

  1. 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

  2. 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

  3. 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.

  4. [Method of multi-resolution 3D image registration by mutual information].

    PubMed

    Ren, Haiping; Wu, Wenkai; Yang, Hu; Chen, Shengzu

    2002-12-01

    Maximization of mutual information is a powerful criterion for 3D medical image registration, allowing robust and fully accurate automated rigid registration of multi-modal images in a various applications. In this paper, a method based on normalized mutual information for 3D image registration was presented on the images of CT, MR and PET. Powell's direction set method and Brent's one-dimensional optimization algorithm were used as optimization strategy. A multi-resolution approach is applied to speedup the matching process. For PET images, pre-procession of segmentation was performed to reduce the background artefacts. According to the evaluation by the Vanderbilt University, Sub-voxel accuracy in multi-modality registration had been achieved with this algorithm. PMID:12561358

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Diffusion tensor image registration using polynomial expansion

    NASA Astrophysics Data System (ADS)

    Wang, Yuanjun; Chen, Zengai; Nie, Shengdong; Westin, Carl-Fredrik

    2013-09-01

    In this paper, we present a deformable registration framework for the diffusion tensor image (DTI) using polynomial expansion. The use of polynomial expansion in image registration has previously been shown to be beneficial due to fast convergence and high accuracy. However, earlier work was developed only for 3D scalar medical image registration. In this work, it is shown how polynomial expansion can be applied to DTI registration. A new measurement is proposed for DTI registration evaluation, which seems to be robust and sensitive in evaluating the result of DTI registration. We present the algorithms for DTI registration using polynomial expansion by the fractional anisotropy image, and an explicit tensor reorientation strategy is inherent to the registration process. Analytic transforms with high accuracy are derived from polynomial expansion and used for transforming the tensor's orientation. Three measurements for DTI registration evaluation are presented and compared in experimental results. The experiments for algorithm validation are designed from simple affine deformation to nonlinear deformation cases, and the algorithms using polynomial expansion give a good performance in both cases. Inter-subject DTI registration results are presented showing the utility of the proposed method.

  10. EVolution: an edge-based variational method for non-rigid multi-modal image registration

    NASA Astrophysics Data System (ADS)

    de Senneville, B. Denis; Zachiu, C.; Ries, M.; Moonen, C.

    2016-10-01

    Image registration is part of a large variety of medical applications including diagnosis, monitoring disease progression and/or treatment effectiveness and, more recently, therapy guidance. Such applications usually involve several imaging modalities such as ultrasound, computed tomography, positron emission tomography, x-ray or magnetic resonance imaging, either separately or combined. In the current work, we propose a non-rigid multi-modal registration method (namely EVolution: an edge-based variational method for non-rigid multi-modal image registration) that aims at maximizing edge alignment between the images being registered. The proposed algorithm requires only contrasts between physiological tissues, preferably present in both image modalities, and assumes deformable/elastic tissues. Given both is shown to be well suitable for non-rigid co-registration across different image types/contrasts (T1/T2) as well as different modalities (CT/MRI). This is achieved using a variational scheme that provides a fast algorithm with a low number of control parameters. Results obtained on an annotated CT data set were comparable to the ones provided by state-of-the-art multi-modal image registration algorithms, for all tested experimental conditions (image pre-filtering, image intensity variation, noise perturbation). Moreover, we demonstrate that, compared to existing approaches, our method possesses increased robustness to transient structures (i.e. that are only present in some of the images).

  11. 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.

  12. Protein-ligand binding affinity by nonequilibrium free energy methods.

    PubMed

    Cossins, Benjamin P; Foucher, Sebastien; Edge, Colin M; Essex, Jonathan W

    2008-11-27

    Nonequilibrium (NE) free energy methods are embarrassingly parallel and may be very conveniently run on desktop computers using distributed computing software. In recent years there has been a proliferation of NE methods, but these approaches have barely, if at all, been used in the context of calculating protein-ligand binding free energies. In a recent study by these authors, different combinations of NE methods with various test systems were compared and protocols identified which yielded results as accurate as replica exchange thermodynamic integration (RETI). The NE approaches, however, lend themselves to extensive parallelization through the use of distributed computing. Here the best performing of those NE protocols, a replica exchange method using Bennett's acceptance ratio as the free energy estimator (RENE), is applied to two sets of congeneric inhibitors bound to neuraminidase and cyclooxygenase-2. These protein-ligand systems were originally studied with RETI, giving results to which NE and RENE simulations are compared. These NE calculations were carried out on a large, highly distributed group of low-performance desktop computers which are part of a Condor pool. RENE was found to produce results of a predictive quality at least as good as RETI in less than half the wall clock time. However, non-RE NE results were found to be far less predictive. In addition, the RENE method successfully identified a localized region of rapidly changing free energy gradients without the need for prior investigation. These results suggest that the RENE protocol is appropriate for use in the context of predicting protein-ligand binding free energies and that it can offer advantages over conventional, equilibrium approaches. PMID:18973369

  13. Deformable registration using scale space keypoints

    NASA Astrophysics Data System (ADS)

    Moradi, Mehdi; Abolmaesoumi, Purang; Mousavi, Parvin

    2006-03-01

    In this paper, we describe a new methodology for keypoint-based affine and deformable medical image registration. This fast and computationally efficient method is automatic and does not rely on segmentation of images. The keypoint pixels used in this technique are extreme points in the scale space and are characterized by descriptor vectors which summarize the intensity gradient profile of the surrounding pixels. For each of the keypoints in the scene image, a corresponding keypoint is identified in the model image using the feature space nearest neighbor criteria. For deformable registration, B-splines are used to extrapolate a regular deformation grid for all of the pixels in the scene image based on the relative displacement vectors of the corresponding pairs. This approach results in a fast and accurate registration in the brain MRI images (an average target registration error of less than 2mm was acquired). We have also studied the affine registration problem in the liver ultrasound and brain MRI images and have acquired acceptable registrations using a mean square solution for affine parameters based on only around 30 corresponding keypoint pairs.

  14. Semiautomatic Registration of Pre- and Postbrain Tumor Resection Laser Range Data: Method and Validation

    PubMed Central

    Ding, Siyi; Miga, Michael I.; Noble, Jack H.; Cao, Aize; Dumpuri, Prashanth; Thompson, Reid C.

    2009-01-01

    This paper presents a semiautomatic method for the registration of images acquired during surgery with a tracked laser range scanner (LRS). This method, which relies on the registration of vessels that can be visualized in the pre- and the postresection images, is a component of a larger system designed to compute brain shift that occurs during tumor resection cases. Because very large differences between pre- and postresection images are typically observed, the development of fully automatic methods to register these images is difficult. The method presented herein is semiautomatic and requires only the identification of a number of points along the length of the vessels. Vessel segments joining these points are then automatically identified using an optimal path finding algorithm that relies on intensity features extracted from the images. Once vessels are identified, they are registered using a robust point-based nonrigid registration algorithm. The transformation computed with the vessels is then applied to the entire image. This permits establishment of a complete correspondence between the pre- and post-3-D LRS data. Experiments show that the method is robust to operator errors in localizing homologous points and a quantitative evaluation performed on ten surgical cases shows submillimetric registration accuracy. PMID:19272895

  15. Interpolation method for accurate affinity ranking of arrayed ligand-analyte interactions.

    PubMed

    Schasfoort, Richard B M; Andree, Kiki C; van der Velde, Niels; van der Kooi, Alex; Stojanović, Ivan; Terstappen, Leon W M M

    2016-05-01

    The values of the affinity constants (kd, ka, and KD) that are determined by label-free interaction analysis methods are affected by the ligand density. This article outlines a surface plasmon resonance (SPR) imaging method that yields high-throughput globally fitted affinity ranking values using a 96-plex array. A kinetic titration experiment without a regeneration step has been applied for various coupled antibodies binding to a single antigen. Globally fitted rate (kd and ka) and dissociation equilibrium (KD) constants for various ligand densities and analyte concentrations are exponentially interpolated to the KD at Rmax = 100 RU response level (KD(R100)).

  16. A comparison of rigid registration methods for prostate localization on CBCT and the dependence on rectum distension

    NASA Astrophysics Data System (ADS)

    Boydev, C.; Pasquier, D.; Derraz, F.; Peyrodie, L.; Taleb-Ahmed, A.; Thiran, J. P.

    2014-03-01

    We evaluated automatic three-dimensional intensity-based rigid registration (RR) methods for prostate localization on CBCT scans and studied the impact of rectum distension on registration quality. 106 CBCT scans of 9 prostate patients were used. Each one was registered to the planning computed tomography (CT) scan using different methods: (a) global registration, (b) pelvis bony structure registration, (c) bony registration refined by a local prostate registration using the CT clinical target volume (CTV) expanded with 1, 3, 5, 8, 10, 12, 15 or 20-mm margin. Automatic CBCT contours were generated after propagation of the manual CT contours. To evaluate results, a radiation oncologist was asked to manually delineate the CTV on the CBCT scans (gold standard). The Dice similarity coefficients between propagated and manual CBCT contours were calculated.

  17. 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.

  18. 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.

  19. Registration of ultrasound echography for intraoperative use: a newly developed multiproperty method

    NASA Astrophysics Data System (ADS)

    Hata, Nobuhiko; Suzuki, Makoto; Dohi, Takeyoshi; Iseki, Hiroshi; Takakura, Kintomo; Hashimoto, Daijo

    1994-09-01

    Nowadays, several studies on 3D medical image registration are being investigated. The main purpose of these studies is to integrate complimentary information provided by different modalities. This paper describes a newly developed registration method of ultrasound echography to 3D medical image. The registration process consists of two stages. In the first stage, a registration process of the ultrasound echography to the pre- operative 3D images is performed using a position sensor. This is a rigid transformation, which can't provide a perfect match because the intra-operative organ is deformed or moved. The second step is a local matching process, where the current position of the ultrasound echography is approximated with a search-based surface matching algorithm. We used the 3D chamfer matching for this approximation. In this method, a goodness-of- match function, i.e., generalized distance, that rates the geometrical transformation is computed and minimized. In a preliminary experiment, the search-based matching process was examined. The algorithm and its accuracy were evaluated with an artificial transformed set of coordinates given as the initial guess. We also performed a clinical application and results confirmed the suitability of this method to clinical use.

  20. 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.

  1. Theoretical study for the electron affinities of negative ions with the MCDHF method

    NASA Astrophysics Data System (ADS)

    Li, Junqin; Zhao, Zilong; Andersson, Martin; Zhang, Xuemei; Chen, Chongyang

    2012-08-01

    Systematic theoretical calculations based on the multi-configuration Dirac-Hartree-Fock method have been carried out for the electron affinities of anions of the elements of group III (B, Al, Ga, In and Tl), group IV (C, Si, Ge, Sn and Pb), group V (N, P and As), group VI (O, S, Se, Te and Po) and group VII (F, Cl, Br, I and At) by studying the ground energies of neutral atoms and their corresponding negative ions. The differences between the calculated total energies of the neutral atom and its anion were used to obtain the electron affinities. We discuss in detail the effects of configuration interaction, investigate the importance of including different types of correlations and check the impact of the higher order relativistic corrections on electron affinities. Our calculated electron affinities are compared with experimental and other available theoretical results. The present studies are the first systematic studies of all these elements. We give the first theoretical values for the affinities of elements Se, Te, Po and At; thereinto, there is no experimental value for elements Po and At.

  2. An Improved InSAR Image Co-Registration Method for Pairs with Relatively Big Distortions or Large Incoherent Areas.

    PubMed

    Chen, Zhenwei; Zhang, Lei; Zhang, Guo

    2016-09-17

    Co-registration is one of the most important steps in interferometric synthetic aperture radar (InSAR) data processing. The standard offset-measurement method based on cross-correlating uniformly distributed patches takes no account of specific geometric transformation between images or characteristics of ground scatterers. Hence, it is inefficient and difficult to obtain satisfying co-registration results for image pairs with relatively big distortion or large incoherent areas. Given this, an improved co-registration strategy is proposed in this paper which takes both the geometric features and image content into consideration. Firstly, some geometric transformations including scale, flip, rotation, and shear between images were eliminated based on the geometrical information, and the initial co-registration polynomial was obtained. Then the registration points were automatically detected by integrating the signal-to-clutter-ratio (SCR) thresholds and the amplitude information, and a further co-registration process was performed to refine the polynomial. Several comparison experiments were carried out using 2 TerraSAR-X data from the Hong Kong airport and 21 PALSAR data from the Donghai Bridge. Experiment results demonstrate that the proposed method brings accuracy and efficiency improvements for co-registration and processing abilities in the cases of big distortion between images or large incoherent areas in the images. For most co-registrations, the proposed method can enhance the reliability and applicability of co-registration and thus promote the automation to a higher level.

  3. An Improved InSAR Image Co-Registration Method for Pairs with Relatively Big Distortions or Large Incoherent Areas.

    PubMed

    Chen, Zhenwei; Zhang, Lei; Zhang, Guo

    2016-01-01

    Co-registration is one of the most important steps in interferometric synthetic aperture radar (InSAR) data processing. The standard offset-measurement method based on cross-correlating uniformly distributed patches takes no account of specific geometric transformation between images or characteristics of ground scatterers. Hence, it is inefficient and difficult to obtain satisfying co-registration results for image pairs with relatively big distortion or large incoherent areas. Given this, an improved co-registration strategy is proposed in this paper which takes both the geometric features and image content into consideration. Firstly, some geometric transformations including scale, flip, rotation, and shear between images were eliminated based on the geometrical information, and the initial co-registration polynomial was obtained. Then the registration points were automatically detected by integrating the signal-to-clutter-ratio (SCR) thresholds and the amplitude information, and a further co-registration process was performed to refine the polynomial. Several comparison experiments were carried out using 2 TerraSAR-X data from the Hong Kong airport and 21 PALSAR data from the Donghai Bridge. Experiment results demonstrate that the proposed method brings accuracy and efficiency improvements for co-registration and processing abilities in the cases of big distortion between images or large incoherent areas in the images. For most co-registrations, the proposed method can enhance the reliability and applicability of co-registration and thus promote the automation to a higher level. PMID:27649207

  4. An Improved InSAR Image Co-Registration Method for Pairs with Relatively Big Distortions or Large Incoherent Areas

    PubMed Central

    Chen, Zhenwei; Zhang, Lei; Zhang, Guo

    2016-01-01

    Co-registration is one of the most important steps in interferometric synthetic aperture radar (InSAR) data processing. The standard offset-measurement method based on cross-correlating uniformly distributed patches takes no account of specific geometric transformation between images or characteristics of ground scatterers. Hence, it is inefficient and difficult to obtain satisfying co-registration results for image pairs with relatively big distortion or large incoherent areas. Given this, an improved co-registration strategy is proposed in this paper which takes both the geometric features and image content into consideration. Firstly, some geometric transformations including scale, flip, rotation, and shear between images were eliminated based on the geometrical information, and the initial co-registration polynomial was obtained. Then the registration points were automatically detected by integrating the signal-to-clutter-ratio (SCR) thresholds and the amplitude information, and a further co-registration process was performed to refine the polynomial. Several comparison experiments were carried out using 2 TerraSAR-X data from the Hong Kong airport and 21 PALSAR data from the Donghai Bridge. Experiment results demonstrate that the proposed method brings accuracy and efficiency improvements for co-registration and processing abilities in the cases of big distortion between images or large incoherent areas in the images. For most co-registrations, the proposed method can enhance the reliability and applicability of co-registration and thus promote the automation to a higher level. PMID:27649207

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Automatic SAR and optical images registration method based on improved SIFT

    NASA Astrophysics Data System (ADS)

    Yue, Chunyu; Jiang, Wanshou

    2014-10-01

    An automatic SAR and optical images registration method based on improved SIFT is proposed in this paper, which is a two-step strategy, from rough to accuracy. The geometry relation of images is first constructed by the geographic information, and images are arranged based on the elevation datum plane to eliminate rotation and resolution differences. Then SIFT features extracted by the dominant direction improved SIFT from two images are matched by SSIM as similar measure according to structure information of the SIFT feature. As rotation difference is eliminated in images of flat area after rough registration, the number of correct matches and correct matching rate can be increased by altering the feature orientation assignment. And then, parallax and angle restrictions are introduced to improve the matching performance by clustering analysis in the angle and parallax domains. Mapping the original matches to the parallax feature space and rotation feature space in sequence, which are established by the custom defined parallax parameters and rotation parameters respectively. Cluster analysis is applied in the parallax feature space and rotation feature space, and the relationship between cluster parameters and matching result is analysed. Owing to the clustering feature, correct matches are retained. Finally, the perspective transform parameters for the registration are obtained by RANSAC algorithm with removing the false matches simultaneously. Experiments show that the algorithm proposed in this paper is effective in the registration of SAR and optical images with large differences.

  11. A deformable image registration method to handle distended rectums in prostate cancer radiotherapy

    SciTech Connect

    Gao Song; Zhang Lifei; Wang He; Crevoisier, Renaud de; Kuban, Deborah D.; Mohan, Radhe; Dong Lei

    2006-09-15

    In image-guided adaptive radiotherapy, it is important to have the capability to automatically and accurately delineate the rectal wall, which is a major dose-limiting organ in prostate cancer radiotherapy. As image registration is a process to find the spatial correspondence between two images, a major challenge in intensity-based deformable image registration is to deal with the situation where no correspondence exists for some objects between the two images to be registered. One example is the variation of rectal contents due to the presence and absence of bowel gas. The intensity-based deformable image registration methods alone cannot create the correct spatial transformation if there is no correspondence between the source and target images. In this study we implemented an automatic image intensity modification procedure to create artificial gas pockets in the planning computed tomography (CT) images. A diffusion-based deformable image registration algorithm was developed to use an adaptive smoothing algorithm to better handle large organ deformations. The process was tested in 15 prostate cancer cases and 30 daily CT images containing the largest distended rectums. The manually delineated rectums agreed well with the autodelineated rectums when using the image-intensity modification procedure.

  12. A method for registration and model-based segmentation of Doppler ultrasound images

    NASA Astrophysics Data System (ADS)

    Kalinić, Hrvoje; Lončarić, Sven; Čikeš, Maja; Milicic, Davor; Čikeš, Ivo; Sutherland, George; Bijnens, Bart

    2009-02-01

    Morphological changes of Doppler ultrasound images are an important source of information for diagnosis of cardiovascular diseases. Quantification of these flow profiles requires segmentation of the ultrasound images. In this article, we propose a new model-based method for segmentation of (aortic outflow) velocity profiles. The method is based on a procedure for registration using a geometric transformation specifically designed for matching Doppler ultrasound profiles. After manual segmentation of a model image, the model image is temporarily registered to a new image using two manually defined points in time. Next, a non-rigid registration was carried out in the velocity direction. As a similarfity measure normalized mutual information is used, while optimization is performed by a genetic algorithm. The registration method is experimentally validated using an in-silico image phantom, and showed an accuracy of 5.4%. The model based on segmentation is evaluated in a seris of aortic outflow Doppler ultrasound images from 30 normal volunteers. Comparing the automated method to the manual delineation by an expert cardiologist the method proved accurate to 6.6%. The experimental results confirm the accuracy of the approach and shows that the method can be used for the segmentation of the clinically obtained aortic outflow velocity profiles.

  13. Atlas to patient registration with brain tumor based on a mesh-free method.

    PubMed

    Diaz, Idanis; Boulanger, Pierre

    2015-08-01

    Brain atlas to patient registration in the presence of tumors is a challenging task because its presence cause brain structure deformations and introduce large intensity variation between the affected areas. This large dissimilarity affects the results of traditional registration methods based on intensity or shape similarities. In order to overcome these problems, we propose a novel method that brings closer the atlas and the patient's image by simulating the mechanical behavior of brain deformation under a tumor pressure. The proposed method use a mesh-free total Lagrangian Explicit Dynamic algorithm for the simulation of atlas deformation and a data driven model of the tumor using multi-modal MRI segmentation. Experimental results look structurally very similar to the patient's image and outperform two of the top ranking algorithms.

  14. Immobilized Metal Affinity Electrophoresis: A Novel Method of Capturing Phosphoproteins by Electrophoresis

    PubMed Central

    Lee, Bao-Shiang; Lasanthi, G.D.; Jayathilaka, P.; Huang, Jin-Sheng; Gupta, Shalini

    2008-01-01

    An immobilized metal affinity electrophoresis (IMAEP) method is described here. In this method, metal ions are immobilized in a native polyacrylamide gel to capture phosphoproteins. The capture of phosphoproteins by IMAEP is demonstrated with immobilized metals like iron, aluminum, manganese, or titanium. In the case studies, phosphoproteins α-casein, β-casein, and phosvitin are successfully extracted from a protein mixture by IMAEP. PMID:19137092

  15. 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.

  16. 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)

  17. 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.

  18. 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

  19. 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

  20. 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

  1. [Research on non-rigid medical image registration algorithm based on SIFT feature extraction].

    PubMed

    Wang, Anna; Lu, Dan; Wang, Zhe; Fang, Zhizhen

    2010-08-01

    In allusion to non-rigid registration of medical images, the paper gives a practical feature points matching algorithm--the image registration algorithm based on the scale-invariant features transform (Scale Invariant Feature Transform, SIFT). The algorithm makes use of the image features of translation, rotation and affine transformation invariance in scale space to extract the image feature points. Bidirectional matching algorithm is chosen to establish the matching relations between the images, so the accuracy of image registrations is improved. On this basis, affine transform is chosen to complement the non-rigid registration, and normalized mutual information measure and PSO optimization algorithm are also chosen to optimize the registration process. The experimental results show that the method can achieve better registration results than the method based on mutual information.

  2. 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

  3. A Lyapunov method for stability analysis of piecewise-affine systems over non-invariant domains

    NASA Astrophysics Data System (ADS)

    Rubagotti, Matteo; Zaccarian, Luca; Bemporad, Alberto

    2016-05-01

    This paper analyses stability of discrete-time piecewise-affine systems, defined on possibly non-invariant domains, taking into account the possible presence of multiple dynamics in each of the polytopic regions of the system. An algorithm based on linear programming is proposed, in order to prove exponential stability of the origin and to find a positively invariant estimate of its region of attraction. The results are based on the definition of a piecewise-affine Lyapunov function, which is in general discontinuous on the boundaries of the regions. The proposed method is proven to lead to feasible solutions in a broader range of cases as compared to a previously proposed approach. Two numerical examples are shown, among which a case where the proposed method is applied to a closed-loop system, to which model predictive control was applied without a-priori guarantee of stability.

  4. 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.

  5. 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

  6. 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.

  7. [Observation of repair of wounded rat skin by affinity histochemical method of SJA].

    PubMed

    Li, Z H; Jin, H L; Zhu, J Z

    1999-02-01

    Time expression of SJA tissue receptors surrounding wounded skin of 40 rats was studied by affinity histochemical method. The results were compared to that by EGFR immunohistochemical method and c-myc situ hydridization method. It was observed that SJA receptors began to decrease after the skin was injured and reached the lowest quantities in 15 minutes. After that, they began to increase and reached the highest quantities in 2 hours. It needs to be further studied whether there is the correlation between SJA receptors and EGFR has the function of repairing wounded skin. PMID:12536384

  8. 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

  9. 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

  10. 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

  11. A general method for greatly improving the affinity of antibodies by using combinatorial libraries

    PubMed Central

    Rajpal, Arvind; Beyaz, Nurten; Haber, Lauric; Cappuccilli, Guido; Yee, Helena; Bhatt, Ramesh R.; Takeuchi, Toshihiko; Lerner, Richard A.; Crea, Roberto

    2005-01-01

    Look-through mutagenesis (LTM) is a multidimensional mutagenesis method that simultaneously assesses and optimizes combinatorial mutations of selected amino acids. The process focuses on a precise distribution within one or more complementarity determining region (CDR) domains and explores the synergistic contribution of amino acid side-chain chemistry. LTM was applied to an anti-TNF-α antibody, D2E7, which is a challenging test case, because D2E7 was highly optimized (Kd = 1 nM) by others. We selected and incorporated nine amino acids, representative of the major chemical functionalities, individually at every position in each CDR and across all six CDRs (57 aa). Synthetic oligonucleotides, each introducing one amino acid mutation throughout the six CDRs, were pooled to generate segregated libraries containing single mutations in one, two, and/or three CDRs for each VH and VL domain. Corresponding antibody libraries were displayed on the cell surface of yeast. After positive binding selection, 38 substitutions in 21 CDR positions were identified that resulted in higher affinity binding to TNF-α. These beneficial mutations in both VH and VL were represented in two combinatorial beneficial mutagenesis libraries and selected by FACS to produce a convergence of variants that exhibit between 500- and 870-fold higher affinities. Importantly, these enhanced affinities translate to a 15- to 30-fold improvement in in vitro TNF-α neutralization in an L929 bioassay. Thus, this LTM/combinatorial beneficial mutagenesis strategy generates a comprehensive energetic map of the antibody-binding site in a facile and rapid manner and should be broadly applicable to the affinity maturation of antibodies and other proteins. PMID:15939870

  12. 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

  13. 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.

  14. Advances and applications of binding affinity prediction methods in drug discovery.

    PubMed

    Parenti, Marco Daniele; Rastelli, Giulio

    2012-01-01

    Nowadays, the improvement of R&D productivity is the primary commitment in pharmaceutical research, both in big pharma and smaller biotech companies. To reduce costs, to speed up the discovery process and to increase the chance of success, advanced methods of rational drug design are very helpful, as demonstrated by several successful applications. Among these, computational methods able to predict the binding affinity of small molecules to specific biological targets are of special interest because they can accelerate the discovery of new hit compounds. Here we provide an overview of the most widely used methods in the field of binding affinity prediction, as well as of our own work in developing BEAR, an innovative methodology specifically devised to overtake some limitations in existing approaches. The BEAR method was successfully validated against different biological targets, and proved its efficacy in retrieving active compounds from virtual screening campaigns. The results obtained so far indicate that BEAR may become a leading tool in the drug discovery pipeline. We primarily discuss advantages and drawbacks of each technique and show relevant examples and applications in drug discovery.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. A high accuracy multi-image registration method for tracking MRI-guided robots

    NASA Astrophysics Data System (ADS)

    Shang, Weijian; Fischer, Gregory S.

    2012-02-01

    Recent studies have demonstrated an increasing number of functional surgical robots and other devices operating in the Magnetic Resonance Imaging (MRI) environment. Calibration and tracking of the robotic device is essential during such MRI-guided procedures. A fiducial tracking module is placed on the base or the end effector of the robot to localize it within the scanner, and thus the patient coordinate system. The fiducial frame represents a Z shape and is made of seven tubes filled with high contrast fluid. The frame is highlighted in the MR images and is used in localization. Compared to the former single image registration method, multiple images are used in this algorithm to calculate the position and orientation of the frame, and thus the robot. By using multiple images together, measurement error is reduced and the rigid requirement of slow to acquire high quality of images is not required. Accuracy and performance were evaluated in experiments which were operated with a Philips 3T MRI scanner. Presented is an accuracy comparison of the new method with varied number of images, and a comparison to more traditional single image registration techniques.

  1. 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

  2. 2D/3D registration with the CMA-ES method

    NASA Astrophysics Data System (ADS)

    Gong, Ren Hui; Abolmaesumi, Purang

    2008-03-01

    In this paper, we propose a new method for 2D/3D registration and report its experimental results. The method employs the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) algorithm to search for an optimal transformation that aligns the 2D and 3D data. The similarity calculation is based on Digitally Reconstructed Radiographs (DRRs), which are dynamically generated from the 3D data using a hardware-accelerated technique - Adaptive Slice Geometry Texture Mapping (ASGTM). Three bone phantoms of different sizes and shapes were used to test our method: a long femur, a large pelvis, and a small scaphoid. A collection of experiments were performed to register CT to fluoroscope and DRRs of these phantoms using the proposed method and two prior work, i.e. our previously proposed Unscented Kalman Filter (UKF) based method and a commonly used simplex-based method. The experimental results showed that: 1) with slightly more computation overhead, the proposed method was significantly more robust to local minima than the simplex-based method; 2) while as robust as the UKF-based method in terms of capture range, the new method was not sensitive to the initial values of its exposed control parameters, and has also no special requirement about the cost function; 3) the proposed method was fast and consistently achieved the best accuracies in all compared methods.

  3. Method for determining the temporal response of microbial phosphate transport affinity.

    PubMed Central

    Molot, L A; Brown, E J

    1986-01-01

    Nutrient transport affinities of nutrient-starved microbial populations were measured as initial slopes of plots of limiting-nutrient transport rates versus extracellular limiting-nutrient concentrations. A method was devised for the determination of soluble reactive phosphate (Pi) affinity in Pi-limited continuous culture (aT), which was then used as an indicator of the effects of light/dark cycle (LD) perturbations on the temporal Pi transport abilities of three species of freshwater algae. Cell division was asynchronous for the green alga Selenastrum capricornutum grown in continuous cultures exposed to LD cycles. An apparent rhythm in aT for Pi was greatly affected by the population size parameter. Cell division was phased for the green alga Scenedesmus quadricauda grown in LD continuous culture. A rhythm in aT for Pi was not greatly affected by the biomass parameter. Cell division was also phased in LD continuous culture for the blue-green alga (cyanobacterium) Synechococcus Nägeli, but rhythms in other parameters could not be detected. Synechococcus Nägeli was an extremely efficient Pi transporter at low Pi concentrations in LD continuous culture, and so aT could not be calculated. The results demonstrate that aT is well suited to describing the temporal response of Pi transport in LD-perturbed, Pi-limited continuous culture. PMID:3083772

  4. 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.

  5. 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

  6. A new method of quantitative affinity chromatography and its application to the study of myosin.

    PubMed Central

    Bottomley, R C; Storer, A C; Trayer, I P

    1976-01-01

    A new method of quantifying the interactions between two or three components of an interacting system, one of which is insoluble, is described. The method differs from those previously applied to affinity chromatography systems in that it does not require that elution volumes be measured, but is instead dependent on measurements of the quantity of affinity-bound material. Theoretical expressions are derived for systems in which the acceptor is immobilized. Examples presented to illustrate the validity of the theory are of the latter type and are from studies on the myosin-adenosine nucleotide-PPi system. With Sepharose-myosin columns (myosin covalently coupled to CNBr-activated Sepharose) a dissociation constant of 1.8 muM for ATP4- was found. Data were also obtained under conditions that closely approximate to those found in vivo, i.e. on columns packed with a slurry of Sephadex G-50 and precipitated myosin filaments formed at low ionic strength. The binding of MgATP2-, MgADP-, ATP4- and MgPPi2- to "filamentous" myosin in both two- (myosin and nucleotide) and three- (myosin, nucleotide and PPi) component systems at different temperatures was studied and the dissociation constants obtained agreed well with previously published values. Except for the binding of ATP4- to filamentous myosin at 4 degrees when 85% of the protein was interacting with the nucleotide, much lower values for the number of available sites occupied by the nucleotides were as a routine found in this system. Although this apparent discrepancy is difficult to explain, it is not an anomaly of the theoretical approach and may reflect the present state of understanding of the myosin system. PMID:1008824

  7. 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

  8. 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.

  9. 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.

  10. A fully automatic image-to-world registration method for image-guided procedure with intraoperative imaging updates

    NASA Astrophysics Data System (ADS)

    Li, Senhu; Sarment, David

    2016-03-01

    Image-guided procedure with intraoperative imaging updates has made a big impact on minimally invasive surgery. Compact and mobile CT imaging device combining with current commercial available image guided navigation system is a legitimate and cost-efficient solution for a typical operating room setup. However, the process of manual fiducial-based registration between image and physical spaces (image-to-world) is troublesome for surgeons during the procedure, which results in much procedure interruptions and is the main source of registration errors. In this study, we developed a novel method to eliminate the manual registration process. Instead of using probe to manually localize the fiducials during the surgery, a tracking plate with known fiducial positions relative to the reference coordinates is designed and fabricated through 3D printing technique. The workflow and feasibility of this method has been studied through a phantom experiment.

  11. Supporting registration decisions during 3D medical volume reconstructions

    NASA Astrophysics Data System (ADS)

    Bajcsy, Peter; Lee, Sang-Chul; Clutter, David

    2006-03-01

    We propose a methodology for making optimal registration decisions during 3D volume reconstruction in terms of (a) anticipated accuracy of aligned images, (b) uncertainty of obtained results during the registration process, (c) algorithmic repeatability of alignment procedure, and (d) computational requirements. We researched and developed a web-enabled, web services based, data-driven, registration decision support system. The registration decisions include (1) image spatial size (image sub-area or entire image), (2) transformation model (e.g., rigid, affine or elastic), (3) invariant registration feature (intensity, morphology or a sequential combination of the two), (4) automation level (manual, semi-automated, or fully-automated), (5) evaluations of registration results (multiple metrics and methods for establishing ground truth), and (6) assessment of resources (computational resources and human expertise, geographically local or distributed). Our goal is to provide mechanisms for evaluating the tradeoffs of each registration decision in terms of the aforementioned impacts. First, we present a medical registration methodology for making registration decisions that lead to registration results with well-understood accuracy, uncertainty, consistency and computational complexity characteristics. Second, we have built software tools that enable geographically distributed researchers to optimize their data-driven registration decisions by using web services and supercomputing resources. The support developed for registration decisions about 3D volume reconstruction is available to the general community with the access to the NCSA supercomputing resources. We illustrate performance by considering 3D volume reconstruction of blood vessels in histological sections of uveal melanoma from serial fluorescent labeled paraffin sections labeled with antibodies to CD34 and laminin. The specimens are studied by fluorescence confocal laser scanning microscopy (CLSM) images.

  12. 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.

  13. 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

  14. 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.

  15. A novel affinity-based method for the isolation of highly purified extracellular vesicles

    PubMed Central

    Nakai, Wataru; Yoshida, Takeshi; Diez, Diego; Miyatake, Yuji; Nishibu, Takahiro; Imawaka, Naoko; Naruse, Ken; Sadamura, Yoshifusa; Hanayama, Rikinari

    2016-01-01

    Extracellular vesicles (EVs) such as exosomes and microvesicles serve as messengers of intercellular network, allowing exchange of cellular components between cells. EVs carry lipids, proteins, and RNAs derived from their producing cells, and have potential as biomarkers specific to cell types and even cellular states. However, conventional methods (such as ultracentrifugation or polymeric precipitation) for isolating EVs have disadvantages regarding purity and feasibility. Here, we have developed a novel method for EV purification by using Tim4 protein, which specifically binds the phosphatidylserine displayed on the surface of EVs. Because the binding is Ca2+-dependent, intact EVs can be easily released from Tim4 by adding Ca2+ chelators. Tim4 purification, which we have applied to cell conditioned media and biofluids, is capable of yielding EVs of a higher purity than those obtained using conventional methods. The lower contamination found in Tim4-purified EV preparations allows more EV-specific proteins to be detected by mass spectrometry, enabling better characterization and quantification of different EV populations’ proteomes. Tim4 protein can also be used as a powerful tool for quantification of EVs in both ELISA and flow cytometry formats. Thus, the affinity of Tim4 for EVs will find abundant applications in EV studies. PMID:27659060

  16. An Extended Affinity Propagation Clustering Method Based on Different Data Density Types

    PubMed Central

    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

  17. 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.

  18. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

    PubMed Central

    Genheden, Samuel; Ryde, Ulf

    2015-01-01

    Introduction: The molecular mechanics energies combined with the Poisson–Boltzmann or generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods are popular approaches to estimate the free energy of the binding of small ligands to biological macromolecules. They are typically based on molecular dynamics simulations of the receptor–ligand complex and are therefore intermediate in both accuracy and computational effort between empirical scoring and strict alchemical perturbation methods. They have been applied to a large number of systems with varying success. Areas covered: The authors review the use of MM/PBSA and MM/GBSA methods to calculate ligand-binding affinities, with an emphasis on calibration, testing and validation, as well as attempts to improve the methods, rather than on specific applications. Expert opinion: MM/PBSA and MM/GBSA are attractive approaches owing to their modular nature and that they do not require calculations on a training set. They have been used successfully to reproduce and rationalize experimental findings and to improve the results of virtual screening and docking. However, they contain several crude and questionable approximations, for example, the lack of conformational entropy and information about the number and free energy of water molecules in the binding site. Moreover, there are many variants of the method and their performance varies strongly with the tested system. Likewise, most attempts to ameliorate the methods with more accurate approaches, for example, quantum-mechanical calculations, polarizable force fields or improved solvation have deteriorated the results. PMID:25835573

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  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. A mathematical method for extracting cell secretion rate from affinity biosensors continuously monitoring cell activity.

    PubMed

    Gao, Yandong; Zhou, Qing; Matharu, Zimple; Liu, Ying; Kwa, Timothy; Revzin, Alexander

    2014-03-01

    Our laboratory has previously developed miniature aptasensors that may be integrated at the site of a small group of cells for continuous detection of cell secreted molecules such as inflammatory cytokine interferon gamma (IFN-γ). In a system such as this, the signal measured at the sensor surfaces is a complex function of transport, reaction, as well as of cellular activity. Herein, we report on the development of a mathematical framework for extracting cell production rates from binding curves generated with affinity biosensors. This framework consisted of a diffusion-reaction model coupled to a root finding algorithm for determining cell production rates values causing convergence of a predetermined criterion. To experimentally validate model predictions, we deployed a microfluidic device with an integrated biosensor for measuring the IFN-γ release from CD4 T cells. We found close agreement between secretion rate observed theoretically and those observed experimentally. After taking into account the differences in sensor geometry and reaction kinetics, the method for cell secretion rate determination described in this paper may be broadly applied to any biosensor continuously measuring cellular activity.

  7. Assessment of a Nuclear Affinity Labeling Method for Tracking Implanted Mesenchymal Stem Cells

    PubMed Central

    Leiker, Merced; Suzuki, Gen; Iyer, Vijay S.; Canty, John M.; Lee, Techung

    2010-01-01

    Therapeutic implantation of mesenchymal stem cells (MSCs) is entering the realm of clinical trials for several human diseases, and yet much remains uncertain regarding their dynamic distribution and cell fate after in vivo application. Discrepancies in the literature can be attributed in part to the use of different cell labeling/tracking methods and cell administration protocols. To identify a stem cell detection method suitable for myocardial implantation in a large animal model, we experimented on three different MSC labeling methods: adenovirus-mediated expression of enhanced green fluorescence protein (EGFP) and β-galactosidase (LacZ), and nuclear staining with DAPI. Intramuscular and intracoronary administrations of labeled porcine MSCs identified the nuclear affinity dye to be a reliable stem cell tracking marker. Stem cell identification is facilitated by an optimized live cell labeling condition generating bright blue fluorescence sharply confined to the nucleus. DAPI-labeled MSCs retained full viability, ceased proliferation, and exhibited an increased differentiation potential. The labeled MSCs remained fully active in expressing key growth factor and cytokine genes, and notably exhibited enhanced expression of the chemokine receptor CXCR4 and its ligand SDF1, indicating their competency in response to tissue injury. Histological analysis revealed that approximately half a million MSCs or ∼2% of the administered MSCs remained localized in the normal pig heart 2 weeks after coronary infusion. That the vast majority of these identified MSCs were interstitial indicated the ability of MSCs to migrate across the coronary endothelium. No evidence was obtained indicating MSC differentiation to cardiomyocyte. PMID:19069634

  8. 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

  9. 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

  10. Identification of Protein Partners in Mycobacteria Using a Single-Step Affinity Purification Method

    PubMed Central

    Cysewski, Dominik; Stoduś, Krystian; Kowalska, Katarzyna; Dziembowski, Andrzej

    2014-01-01

    Tuberculosis is a leading cause of death in developing countries. Efforts are being made to both prevent its spread and improve curability rates. Understanding the biology of the bacteria causing the disease, Mycobacterium tuberculosis (M. tuberculosis), is thus vital. We have implemented improved screening methods for protein–protein interactions based on affinity purification followed by high-resolution mass spectrometry. This method can be efficiently applied to both medium- and high-throughput studies aiming to characterize protein–protein interaction networks of tubercle bacilli. Of the 4 tested epitopes FLAG, enhanced green fluorescent protein (eGFP), protein A and haemagglutinin, the eGFP tag was found to be most useful on account of its easily monitored expression and its ability to function as a simultaneous tool for subcellular localization studies. It presents a relatively low background with cost-effective purification. RNA polymerase subunit A (RpoA) was used as a model for investigation of a large protein complex. When used as bait, it co-purified with all remaining RNA polymerase core subunits as well as many accessory proteins. The amount of RpoA strongly correlated with the amount of quantification peptide used as part of the tagging system in this study (SH), making it applicable for semi-quantification studies. Interactions between the components of the RpoA-eGFP protein complex were further confirmed using protein cross-linking. Dynamic changes in the composition of protein complexes under induction of UV damage were observed when UvrA-eGFP expressing cells treated with UV light were used to co-purify UvrA interaction partners. PMID:24664103

  11. Identification of protein partners in mycobacteria using a single-step affinity purification method.

    PubMed

    Płociński, Przemysław; Laubitz, Daniel; Cysewski, Dominik; Stoduś, Krystian; Kowalska, Katarzyna; Dziembowski, Andrzej

    2014-01-01

    Tuberculosis is a leading cause of death in developing countries. Efforts are being made to both prevent its spread and improve curability rates. Understanding the biology of the bacteria causing the disease, Mycobacterium tuberculosis (M. tuberculosis), is thus vital. We have implemented improved screening methods for protein-protein interactions based on affinity purification followed by high-resolution mass spectrometry. This method can be efficiently applied to both medium- and high-throughput studies aiming to characterize protein-protein interaction networks of tubercle bacilli. Of the 4 tested epitopes FLAG, enhanced green fluorescent protein (eGFP), protein A and haemagglutinin, the eGFP tag was found to be most useful on account of its easily monitored expression and its ability to function as a simultaneous tool for subcellular localization studies. It presents a relatively low background with cost-effective purification. RNA polymerase subunit A (RpoA) was used as a model for investigation of a large protein complex. When used as bait, it co-purified with all remaining RNA polymerase core subunits as well as many accessory proteins. The amount of RpoA strongly correlated with the amount of quantification peptide used as part of the tagging system in this study (SH), making it applicable for semi-quantification studies. Interactions between the components of the RpoA-eGFP protein complex were further confirmed using protein cross-linking. Dynamic changes in the composition of protein complexes under induction of UV damage were observed when UvrA-eGFP expressing cells treated with UV light were used to co-purify UvrA interaction partners. PMID:24664103

  12. 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

  13. 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

  14. 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.

  15. 32 CFR 1615.1 - Registration.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM ADMINISTRATION OF 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...

  16. 32 CFR 1615.1 - Registration.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM ADMINISTRATION OF 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...

  17. 32 CFR 1615.1 - Registration.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM ADMINISTRATION OF 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...

  18. 32 CFR 1615.1 - Registration.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM ADMINISTRATION OF 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...

  19. Injury pattern in youth team handball: a comparison of two prospective registration methods.

    PubMed

    Olsen, O-E; Myklebust, G; Engebretsen, L; Bahr, R

    2006-12-01

    The purpose of this study was to examine the injury incidence and pattern of injuries in youth female and male team handball players using two different prospective registration methods; match reports (90 teams, 1080 players) and coach reports (34 teams, 428 players). A total of 118 injuries were recorded by the coach report, of which 93 (79%) were acute injuries (incidence training: 0.9+/-0.16 injuries/1000 player hours; matches: 9.9+/-1.26; rate ratio vs training: 10.8 [95% confidence interval (CI) 7.0-16.6]; P<0.0001) and 25 (21%) were overuse injuries. Knee (26%) and ankle (24%) injuries accounted for half of the acute injuries (training: 0.5+/-0.12 injuries/1000/h; matches: 4.4+/-0.84; rate ratio vs training: 8.0 (95% CI 4.5-14.5); P<0.0001). No gender difference was found in the injury rate (rate ratio female vs male: 1.3 (95% CI 0.8-2.1); P=0.40). Most of the injuries occurred in the attacking phase by back or wing players doing a plant-and-cut, landing or turning movement, and more than half in contact situations with the opponent. Similar results were observed for acute match injuries in the match report. These results indicate that the rate of injuries in youth team handball is as high as at the senior level, and prevention should focus on knee and ankle injuries. The coach report seems to be the best method to register injuries in youth team handball to provide a full spectrum of injuries according to their type, incidence and severity. PMID:17121645

  20. 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.

  1. 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.

  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. 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

  5. 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.

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

    SciTech Connect

    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.

  7. 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

  8. 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.

  9. Multifunction extension of simplex optimization method for mutual information-based registration of ultrasound volumes

    NASA Astrophysics Data System (ADS)

    Zagrodsky, Vladimir; Shekhar, Raj; Cornhill, J. Fredrick

    2001-07-01

    Mutual information has been demonstrated to be an accurate and reliable criterion function to perform registration of medical data. Due to speckle noise, ultrasound volumes do not provide a smooth mutual information function. Consequently the optimization technique used must be robust enough to avoid local maxima and converge on the desired global maximum eventually. While the well-known downhill simplex optimization uses a single criterion function, our extension to multi-function optimization uses three criterion functions, namely mutual information computed at three levels of intensity quantization and hence three degrees of noise suppression. Registration was performed with rigid as well as simple non-rigid transformation modes for real-time 3D ultrasound datasets of the left ventricle. Pairs of frames corresponding to the most stationary end- diastolic cardiac phase were chosen, and an initial misalignment was artificially introduced between them. The multi-function simplex optimization reduced the failure rate by a factor of two in comparison to the standard simplex optimization, while the average accuracy for the successful cases was unchanged. A more robust registration resulted form the parallel use of criterion functions. The additional computational cost was negligible, as each of the three implementations of the mutual information used the same joint histogram and required no extra spatial transformation.

  10. 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)

  11. 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

  12. 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

  13. 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

  14. DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems.

    PubMed

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

    2014-07-21

    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.

  15. 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

  16. 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.

  17. [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

  18. 32 CFR 1615.1 - Registration.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... registration card or other method of registration prescribed by the Director of Selective Service by a person... the records (master computer file) of the Selective Service System. Registration is completed when... Director include completing a Selective Service Registration Card at a classified Post Office,...

  19. 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

  20. 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

  1. 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

  2. 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 structures

  3. 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

  4. 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

  5. Affine projective Osserman structures

    NASA Astrophysics Data System (ADS)

    Gilkey, P.; Nikčević, S.

    2013-08-01

    By considering the projectivized spectrum of the Jacobi operator, we introduce the concept of projective Osserman manifold in both the affine and in the pseudo-Riemannian settings. If M is an affine projective Osserman manifold, then the deformed Riemannian extension metric on the cotangent bundle is both spacelike and timelike projective Osserman. Since any rank-1-symmetric space is affine projective Osserman, this provides additional information concerning the cotangent bundle of a rank-1 Riemannian symmetric space with the deformed Riemannian extension metric. We construct other examples of affine projective Osserman manifolds where the Ricci tensor is not symmetric and thus the connection in question is not the Levi-Civita connection of any metric. If the dimension is odd, we use methods of algebraic topology to show the Jacobi operator of an affine projective Osserman manifold has only one non-zero eigenvalue and that eigenvalue is real.

  6. 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

  7. A method for small molecule microarray-based screening for the rapid discovery of affinity-based probes.

    PubMed

    Shi, Haibin; Uttamchandani, Mahesh; Yao, Shao Q

    2010-01-01

    We describe herein a new method for the high-throughput identification of affinity-based probes (AfBPs) using a small molecule microarray (SMM) approach. A hydroxylethylene-based small molecule library was first generated by solid-phase combinatorial synthesis. The library was tagged with biotin to facilitate immobilization on avidin-coated slides. Preliminary screening with γ-secretase (both the recombinantly purified protein as well as cellular lysates overexpressing the enzyme) was carried out, in order to identify potential small molecule binders, which were subsequently redesigned into AfBPs. Several specific and potent probes for γ-secretase were thus identified through the binding profiles observed on the SMMs. The SMM platform was able to sensitively and conveniently report activity-based binding interactions between aspartic proteases and their small molecule inhibitors. This new approach thus provides a potentially more rapid and efficient method for developing AfBPs using SMMs.

  8. 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.

  9. 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.

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

    DOEpatents

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

    2012-08-07

    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.

  11. 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.

  12. Comparative evaluation of multiresolution optimization strategies for multimodality image registration by maximization of mutual information.

    PubMed

    Maes, F; Vandermeulen, D; Suetens, P

    1999-12-01

    Maximization of mutual information of voxel intensities has been demonstrated to be a very powerful criterion for three-dimensional medical image registration, allowing robust and accurate fully automated affine registration of multimodal images in a variety of applications, without the need for segmentation or other preprocessing of the images. In this paper, we investigate the performance of various optimization methods and multiresolution strategies for maximization of mutual information, aiming at increasing registration speed when matching large high-resolution images. We show that mutual information is a continuous function of the affine registration parameters when appropriate interpolation is used and we derive analytic expressions of its derivatives that allow numerically exact evaluation of its gradient. Various multiresolution gradient- and non-gradient-based optimization strategies, such as Powell, simplex, steepest-descent, conjugate-gradient, quasi-Newton and Levenberg-Marquardt methods, are evaluated for registration of computed tomography (CT) and magnetic resonance images of the brain. Speed-ups of a factor of 3 on average compared to Powell's method at full resolution are achieved with similar precision and without a loss of robustness with the simplex, conjugate-gradient and Levenberg-Marquardt method using a two-level multiresolution scheme. Large data sets such as 256(2) x 128 MR and 512(2) x 48 CT images can be registered with subvoxel precision in <5 min CPU time on current workstations. PMID:10709702

  13. Delivery Path Length and Holding Tree Minimization Method of Securities Delivery among the Registration Agencies Connected as Non-Tree

    NASA Astrophysics Data System (ADS)

    Shimamura, Atsushi; Moritsu, Toshiyuki; Someya, Harushi

    To dematerialize the securities such as stocks or cooporate bonds, the securities were registered to account in the registration agencies which were connected as tree. This tree structure had the advantage in the management of the securities those were issued large amount and number of brands of securities were limited. But when the securities such as account receivables or advance notes are dematerialized, number of brands of the securities increases extremely. In this case, the management of securities with tree structure becomes very difficult because of the concentration of information to root of the tree. To resolve this problem, using the graph structure is assumed instead of the tree structure. When the securities are kept with tree structure, the delivery path of securities is unique, but when securities are kept with graph structure, path of delivery is not unique. In this report, we describe the requirement of the delivery path of securities, and we describe selecting method of the path.

  14. High-Throughput Melanin-Binding Affinity and In Silico Methods to Aid in the Prediction of Drug Exposure in Ocular Tissue.

    PubMed

    Reilly, John; Williams, Sarah L; Forster, Cornelia J; Kansara, Viral; End, Peter; Serrano-Wu, Michael H

    2015-12-01

    Drugs possessing the ability to bind to melanin-rich tissue, such as the eye, are linked with higher ocular exposure, and therefore have the potential to affect the efficacy and safety profiles of therapeutics. A high-throughput melanin chromatographic affinity assay has been developed and validated, which has allowed the rapid melanin affinity assessment for a large number of compounds. Melanin affinity of compounds can be quickly assigned as low, medium, or high melanin binders. A high-throughput chromatographic method has been developed and fully validated to assess melanin affinity of pharmaceuticals and has been useful in predicting ocular tissue distribution in vivo studies. The high-throughput experimental approach has also allowed for a specific training set of 263 molecules for a quantitative structure-affinity relationships (QSAR) method to be developed, which has also been shown to be a predictor of ocular tissue exposure. Previous studies have reported the development of in silico QSAR models based on training sets of relatively small and mostly similar compounds; this model covers a broader range of melanin-binding affinities than what has been previously published and identified several physiochemical descriptors to be considered in the design of compounds where melanin-binding modulation is desired.

  15. 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

  16. Cellular recurrent deep network for image registration

    NASA Astrophysics Data System (ADS)

    Alam, M.; Vidyaratne, L.; Iftekharuddin, Khan M.

    2015-09-01

    Image registration using Artificial Neural Network (ANN) remains a challenging learning task. Registration can be posed as a two-step problem: parameter estimation and actual alignment/transformation using the estimated parameters. To date ANN based image registration techniques only perform the parameter estimation, while affine equations are used to perform the actual transformation. In this paper, we propose a novel deep ANN based image rigid registration that combines parameter estimation and transformation as a simultaneous learning task. Our previous work shows that a complex universal approximator known as Cellular Simultaneous Recurrent Network (CSRN) can successfully approximate affine transformations with known transformation parameters. This study introduces a deep ANN that combines a feed forward network with a CSRN to perform full rigid registration. Layer wise training is used to pre-train feed forward network for parameter estimation and followed by a CSRN for image transformation respectively. The deep network is then fine-tuned to perform the final registration task. Our result shows that the proposed deep ANN architecture achieves comparable registration accuracy to that of image affine transformation using CSRN with known parameters. We also demonstrate the efficacy of our novel deep architecture by a performance comparison with a deep clustered MLP.

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. [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

  3. 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

  4. 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.

  5. A gaseous radiochemical method for registration of ionizing radiation and its possible applications in science and economy

    NASA Astrophysics Data System (ADS)

    Lebedev, S. G.; Akulinichev, S. V.; Iljinov, A. S.; Yants, V. E.

    2006-05-01

    This work presents a new possibility of registration of ionizing radiation by the flowing gaseous radiochemical method (FGRM). The specified method uses the property of some solid crystalline lattice materials for a free emission of radioactive isotopes of inert gas atoms formed as a result of nuclear reactions. Generated in an ampoule of the detector, the radioactive inert gases are transported by a gas-carrier into the proportional gas counter of the flowing type, where the decay rate of the radioactive gas species is measured. This quantity is unequivocally related to the flux of particles (neutrons, protons, light and heavy ions) at the location of the ampoule. The method was used to monitor the neutron flux of the pulsed neutron target “RADEX” driven by the linear proton accelerator of INR RAS. Further progress of the FGRM may give rise to possible applications in nuclear physics, astrophysics and medicine, in the nondestructive control of fissionable materials, diagnostics of thermonuclear plasma, monitoring of fluxes and measurement of spectra of bombarding particles.

  6. 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.

  7. Quantitative assessment of mis-registration issues of diffusion tensor imaging (DTI)

    NASA Astrophysics Data System (ADS)

    Li, Yue; Jiang, Hangyi; Mori, Susumu

    2012-02-01

    Image distortions caused by eddy current and patient motion have been two major sources of the mis-registration issues in diffusion tensor imaging (DTI). Numerous registration methods have been proposed to correct them. However, quality control of DTI remains an important issue, because we rarely report how much mis-registration existed and how well they were corrected. In this paper, we propose a method for quantitative reporting of DTI data quality. This registration method minimizes a cost function based on mean square tensor fitting errors. Registration with twelve-parameter full affine transformation is used. From the registration result, distortion and motion parameters are estimated. Because the translation parameters involve both eddy-current-induced image translation and the patient motion, by analyzing the transformation model, we separate them by removing the contributions that are linearly correlated with diffusion gradients. We define the metrics measuring the amounts of distortion, rotation, translation. We tested our method on a database with 64 subjects and found the statistics of each of metrics. Finally we demonstrate that how these statistics can be used for assessing the data quality quantitatively in several examples.

  8. 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.

  9. 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.

  10. System and method for 3-D/3-D registration between non-contrast-enhanced CBCT and contrast-enhanced CT for abdominal aortic aneurysm stenting.

    PubMed

    Miao, Shun; Liao, Rui; Pfister, Marcus; Zhang, Li; Ordy, Vincent

    2013-01-01

    In this paper, we present an image guidance system for abdominal aortic aneurysm stenting, which brings pre-operative 3-D computed tomography (CT) into the operating room by registering it against intra-operative non-contrast-enhanced cone-beam CT (CBCT). Registration between CT and CBCT volumes is a challenging task due to two factors: the relatively low signal-to-noise ratio of the abdominal aorta in CBCT without contrast enhancement, and the drastically different field of view between the two image modalities. The proposed automatic registration method handles the first issue through a fast quasi-global search utilizing surrogate 2-D images, and solves the second problem by relying on neighboring dominant structures of the abdominal aorta (i.e. the spine) for initial coarse alignment, and using a confined and image-processed volume of interest around the abdominal aorta for fine registration. The proposed method is validated offline using 17 clinical datasets, and achieves 1.48 mm target registration error and 100% success rate in 2.83 s. The prototype system has been installed in hospitals for clinical trial and applied in around 30 clinical cases, with 100% success rate reported qualitatively. PMID:24505689

  11. 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.

  12. Registration and measurement of opening and closing jaw movements and rotational mandibular capacity by using the method of electronic axiography.

    PubMed

    Kraljević, Sonja; Pandurić, Josip; Badel, Tomislav; Dulcić, Niksa

    2003-01-01

    The aim of this study was to register and measure lower jaw movements, to analyse the measured length of opening and closing movements and to analyse the rotational mandibular capacity during the maximal opening of the mouth in the position of centric relation. Our objective was to determine the average values for each mandible and temporomandibular joint movement, as well as to determine the accuracy of electronic axiography, while diagnosing temporomandibular joint disorders. A statistical analysis was performed in order to evaluate whether significant differences between the length of the measured movements in asymptomatic and symptomatic subjects could be found. A symptomatic group consisted of 51 subjects with temporomandibular disorders. A control group consisted of 43 subjects without signs and symptoms of temporomandibular joint disorders. Each subject was registered by the GAMMA CADIAX system for registration of position and movement of the lower jaw, which consists of a conventional SAM axiograph, an electronic device for drawing curves by means of a computer. No significant differences were found between the groups of subjects for the measured variables. The results of the length of the mandibular and condyle movements, along with the rotational capacity of the mandible are important, in spite of unreliable indicators of temporomandibular joint function. Description analysis of a graphic recording of mandibular and TMJ movement remains an accurate evaluation method for the determination of TMJ dysfunction.

  13. An ellipse-fitting based method for efficient registration of breast masses on two mammographic views

    SciTech Connect

    Pu Jiantao; Zheng Bin; Leader, Joseph Ken; Gur, David

    2008-02-15

    When reading mammograms, radiologists routinely search for and compare suspicious breast lesions identified on two corresponding craniocaudal (CC) and mediolateral oblique (MLO) views. Automatically identifying and matching the same true-positive breast lesions depicted on two views is an important step for developing successful multiview based computer-aided detection (CAD) schemes. The authors developed a method to automatically register breast areas and detect matching strips of interest used to identify the matched mass regions depicted on CC and MLO views. The method uses an ellipse based model to fit the breast boundary contour (skin line) and set a local Cartesian coordinate system for each view. One intersection point between the major/minor axis and the fitted ellipse perimeter passed through breast boundary is selected as the origin and the majoraxis and the minoraxis of the ellipse are used as the two axis of the Cartesian coordinate system. When a mass is identified on one view, the scheme computes its position in the local coordinate system. Then, the distance is mapped onto the local coordinate of the other view. At the end of the mapped distance a registered centerline of the matching strip is created. The authors established an image database that includes 200 test examinations each depicting one verified mass visible on the two views. They tested whether the registered centerline identified on another view can be used to locate the matched mass region. The experiments show that the average distance between the mass region centers and the registered centerlines was {+-}8.3 mm and in 91% of testing cases the registered centerline actually passes through the matched mass regions. A matching strip width of 47 mm was required to achieve 100% sensitivity for the test database. The results demonstrate the feasibility of the proposed method to automatically identify masses depicted on CC and MLO views, which may improve future development of multiview

  14. An ellipse-fitting based method for efficient registration of breast masses on two mammographic views

    PubMed Central

    Pu, Jiantao; Zheng, Bin; Leader, Joseph Ken; Gur, David

    2008-01-01

    When reading mammograms, radiologists routinely search for and compare suspicious breast lesions identified on two corresponding craniocaudal (CC) and mediolateral oblique (MLO) views. Automatically identifying and matching the same true-positive breast lesions depicted on two views is an important step for developing successful multiview based computer-aided detection (CAD) schemes. The authors developed a method to automatically register breast areas and detect matching strips of interest used to identify the matched mass regions depicted on CC and MLO views. The method uses an ellipse based model to fit the breast boundary contour (skin line) and set a local Cartesian coordinate system for each view. One intersection point between the major/minor axis and the fitted ellipse perimeter passed through breast boundary is selected as the origin and the majoraxis and the minoraxis of the ellipse are used as the two axis of the Cartesian coordinate system. When a mass is identified on one view, the scheme computes its position in the local coordinate system. Then, the distance is mapped onto the local coordinate of the other view. At the end of the mapped distance a registered centerline of the matching strip is created. The authors established an image database that includes 200 test examinations each depicting one verified mass visible on the two views. They tested whether the registered centerline identified on another view can be used to locate the matched mass region. The experiments show that the average distance between the mass region centers and the registered centerlines was ±8.3 mm and in 91% of testing cases the registered centerline actually passes through the matched mass regions. A matching strip width of 47 mm was required to achieve 100% sensitivity for the test database. The results demonstrate the feasibility of the proposed method to automatically identify masses depicted on CC and MLO views, which may improve future development of multiview based

  15. Registration pollution of water by method of modulation intracavity laser spectroscopy

    NASA Astrophysics Data System (ADS)

    Bojko, Sergey; Gamalii, Vladimir F.

    1995-09-01

    In this work, the method of the modulation intracavity laser spectroscopy is shown to be candidate for investigation and quantitative analysis of organic pollutions in water. The test specimen is placed into the cavity of the multimode dye laser. When the Raman scattering line coincides with amplification spectrum of the active medium of the multimode laser the additional gain appears at the Stokes frequency. One can experimentally determine this gain and then determine concentration of pollution. Spectral width of the Raman lines are small (approximately 3 cm-1), therefore a number of organic pollutions may be observed simultaneously. We have investigated stimulated Raman scattering from molecules of peridin (C5H5N) in water. In our conditions concentration sensitivity was 7 IO-4M/1.

  16. 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.

  17. 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

  18. 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...).

  19. Development of a sensitive method for selection of affinity ligand for trypsin using quartz crystal microbalance sensor.

    PubMed

    Bayramoglu, Gulay; Yakup Arica, M

    2012-03-01

    In this work, a new methodology is developed for selection of affinity ligands towards the enzyme "trypsin" using quartz crystals microbalance (QCM) technique. To achieve this goal, the surface amination of gold plated QCM crystals was achieved in 13.56 MHz plasma polymerization system by using ethylenediamine. Three different ligands (i.e., 4-aminobenzamidine, 4-aminobenzoic acid, and phenylalanine) were immobilized on the aminated QCM crystals surface via glutaraldehyde coupling. All three ligand immobilized QCM crystals were characterized and compared under different experimental conditions. It was observed that the benzamidine ligand showed higher affinity to trypsin with a dissociation constant on the order of 1.76 × 10(-9) M, which is within the range of 10(-4)-10(-8) M for affinity ligands. Thus, its selectivity was suitable for purification of trypsin from biological fluids. PMID:21853329

  20. Continuous registration based on computed tomography for breathing motion compensation

    PubMed Central

    Zyłkowski, Jaroslaw; Wróblewski, Tadeusz

    2013-01-01

    Introduction Image guidance for intervention is applied for complex and difficult anatomical regions. Nowadays, it is typically used in neurosurgery, otolaryngology, orthopedics and dentistry. The application of the image-guided system for soft tissues is challenging due to various deformations caused by respiratory motion, tissue elasticity and peristalsis. Aim The main task for the presented approach is continuous registration of preoperative computed tomography (CT) and patient position in the operating room (OR) without touching the patient and compensation of breathing motion. This approach is being developed as a step to image-guided percutaneous liver RF tumor ablation. Material and methods Up to ten integrated radiological markers are placed on the patient's skin before CT scans. Then the anatomical model based on CT images is calculated. Point-to-point registration based on the Horn algorithm during a few breathing cycles is performed using a videometric tracking system. The transformation which corresponds to the minimum fiducial registration error (FRE) is found during the registration and it is treated as the initial transformation for calculating local deformation field of breathing motion compensation based on the spline approach. Results For manual registration of the abdominal phantom, the mean values of target registration error (TRE), fiducial localization error (FLE) and FRE are all below 4 mm for the rigid transformation and are below 1 mm for the affine transformation. For the patient's data they are all below 9 mm and 6 mm, respectively. For the automatic method, different marker configurations have been evaluated while dividing the respiratory cycle into inhale and exhale. Average median values for FRE, TRE rigid estimation and TRE based on spline deformation were 15.56 mm, 0.82 mm and 7.21 mm respectively. Conclusions In this application two registration methods of abdominal preoperative CT anatomical model and physical patient position in

  1. 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

  2. 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.

  3. 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.

  4. 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

    2016-03-04

    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.

  5. 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

  6. 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.

  7. Simple method for Shiga toxin 2e purification by affinity chromatography via binding to the divinyl sulfone group.

    PubMed

    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

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. Comparative study of application accuracy of two frameless neuronavigation systems: experimental error assessment quantifying registration methods and clinically influencing factors.

    PubMed

    Paraskevopoulos, Dimitrios; Unterberg, Andreas; Metzner, Roland; Dreyhaupt, Jens; Eggers, Georg; Wirtz, Christian Rainer

    2010-04-01

    This study aimed at comparing the accuracy of two commercial neuronavigation systems. Error assessment and quantification of clinical factors and surface registration, often resulting in decreased accuracy, were intended. Active (Stryker Navigation) and passive (VectorVision Sky, BrainLAB) neuronavigation systems were tested with an anthropomorphic phantom with a deformable layer, simulating skin and soft tissue. True coordinates measured by computer numerical control were compared with coordinates on image data and during navigation, to calculate software and system accuracy respectively. Comparison of image and navigation coordinates was used to evaluate navigation accuracy. Both systems achieved an overall accuracy of <1.5 mm. Stryker achieved better software accuracy, whereas BrainLAB better system and navigation accuracy. Factors with conspicuous influence (P<0.01) were imaging, instrument replacement, sterile cover drape and geometry of instruments. Precision data indicated by the systems did not reflect measured accuracy in general. Surface matching resulted in no improvement of accuracy, confirming former studies. Laser registration showed no differences compared to conventional pointers. Differences between the two systems were limited. Surface registration may improve inaccurate point-based registrations but does not in general affect overall accuracy. Accuracy feedback by the systems does not always match with true target accuracy and requires critical evaluation from the surgeon.

  13. 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

  14. 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

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

    PubMed Central

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

    2014-01-01

    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

  16. 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

  17. Virtual bite registration using intraoral digital scanning, CT and CBCT: In vitro evaluation of a new method and its implication for orthognathic surgery.

    PubMed

    Nilsson, Johanna; Richards, Robert Geoff; Thor, Andreas; Kamer, Lukas

    2016-09-01

    Three-dimensional (3D) computer-assisted planning requires detailed visualisation of the craniomaxillofacial region and interocclusal relationship. The aim of this study was to establish and evaluate a method to create a 3D model of the craniomaxillofacial region and to adopt intraoral digital scanning to place the lower jaw into a centric relation (CR) without the need of additional plaster casts and model surgery. A standard plastic skull modified by metallic dental wires and brackets was subjected to computed tomography (CT), cone beam computed tomography (CBCT), and intraoral digital scanning. We evaluated two different virtual bite registrations, a digital scan of the buccal dental surfaces and scanning of the wax bites to position the lower jaw into a CR, and assessed the accuracy of the integration of intraoral scanning to the CT/CBCT scans. The mean registration error of corresponding mesh points for the CT and intraoral scanned images was 0.15 ± 0.12 mm, while this error was 0.18 ± 0.13 mm for the CBCT and intraoral scanned images. The mean accuracy of the two virtual bite registrations ranged from 0.41 to 0.49 mm (buccal scan technique) and from 0.65 to 1.3 mm (virtualised wax bite technique). A method for virtual bite registration was developed. It has the potential to eliminate plaster casts and model surgery and may facilitate 3D computer-assisted planning of orthognathic surgery cases.

  18. Virtual bite registration using intraoral digital scanning, CT and CBCT: In vitro evaluation of a new method and its implication for orthognathic surgery.

    PubMed

    Nilsson, Johanna; Richards, Robert Geoff; Thor, Andreas; Kamer, Lukas

    2016-09-01

    Three-dimensional (3D) computer-assisted planning requires detailed visualisation of the craniomaxillofacial region and interocclusal relationship. The aim of this study was to establish and evaluate a method to create a 3D model of the craniomaxillofacial region and to adopt intraoral digital scanning to place the lower jaw into a centric relation (CR) without the need of additional plaster casts and model surgery. A standard plastic skull modified by metallic dental wires and brackets was subjected to computed tomography (CT), cone beam computed tomography (CBCT), and intraoral digital scanning. We evaluated two different virtual bite registrations, a digital scan of the buccal dental surfaces and scanning of the wax bites to position the lower jaw into a CR, and assessed the accuracy of the integration of intraoral scanning to the CT/CBCT scans. The mean registration error of corresponding mesh points for the CT and intraoral scanned images was 0.15 ± 0.12 mm, while this error was 0.18 ± 0.13 mm for the CBCT and intraoral scanned images. The mean accuracy of the two virtual bite registrations ranged from 0.41 to 0.49 mm (buccal scan technique) and from 0.65 to 1.3 mm (virtualised wax bite technique). A method for virtual bite registration was developed. It has the potential to eliminate plaster casts and model surgery and may facilitate 3D computer-assisted planning of orthognathic surgery cases. PMID:27423538

  19. 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.

  20. 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

  1. Two-parameter twisted quantum affine algebras

    NASA Astrophysics Data System (ADS)

    Jing, Naihuan; Zhang, Honglian

    2016-09-01

    We establish Drinfeld realization for the two-parameter twisted quantum affine algebras using a new method. The Hopf algebra structure for Drinfeld generators is given for both untwisted and twisted two-parameter quantum affine algebras, which include the quantum affine algebras as special cases.

  2. 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

  3. 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

  4. 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.

  5. The Isotope-Coded Affinity Tag Method for Quantitative Protein Profile Comparison and Relative Quantitation of Cysteine Redox Modifications.

    PubMed

    Chan, James Chun Yip; Zhou, Lei; Chan, Eric Chun Yong

    2015-11-02

    The isotope-coded affinity tag (ICAT) technique has been applied to measure pairwise changes in protein expression through differential stable isotopic labeling of proteins or peptides followed by identification and quantification using a mass spectrometer. Changes in protein expression are observed when the identical peptide from each of two biological conditions is identified and a difference is detected in the measurements comparing the peptide labeled with the heavy isotope to the one with a normal isotopic distribution. This approach allows the simultaneous comparison of the expression of many proteins between two different biological states (e.g., yeast grown on galactose versus glucose, or normal versus cancer cells). Due to the cysteine-specificity of the ICAT reagents, the ICAT technique has also been applied to perform relative quantitation of cysteine redox modifications such as oxidation and nitrosylation. This unit describes both protein quantitation and profiling of cysteine redox modifications using the ICAT technique.

  6. 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

  7. Analysis of Point Based Image Registration Errors With Applications in Single Molecule Microscopy

    PubMed Central

    Cohen, E. A. K.; Ober, R. J.

    2014-01-01

    We present an asymptotic treatment of errors involved in point-based image registration where control point (CP) localization is subject to heteroscedastic noise; a suitable model for image registration in fluorescence microscopy. Assuming an affine transform, CPs are used to solve a multivariate regression problem. With measurement errors existing for both sets of CPs this is an errors-in-variable problem and linear least squares is inappropriate; the correct method being generalized least squares. To allow for point dependent errors the equivalence of a generalized maximum likelihood and heteroscedastic generalized least squares model is achieved allowing previously published asymptotic results to be extended to image registration. For a particularly useful model of heteroscedastic noise where covariance matrices are scalar multiples of a known matrix (including the case where covariance matrices are multiples of the identity) we provide closed form solutions to estimators and derive their distribution. We consider the target registration error (TRE) and define a new measure called the localization registration error (LRE) believed to be useful, especially in microscopy registration experiments. Assuming Gaussianity of the CP localization errors, it is shown that the asymptotic distribution for the TRE and LRE are themselves Gaussian and the parameterized distributions are derived. Results are successfully applied to registration in single molecule microscopy to derive the key dependence of the TRE and LRE variance on the number of CPs and their associated photon counts. Simulations show asymptotic results are robust for low CP numbers and non-Gaussianity. The method presented here is shown to outperform GLS on real imaging data. PMID:24634573

  8. 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

  9. 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

  10. 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.

  11. 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

  12. Effect of registration on cyclical kinematic data.

    PubMed

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

    2010-08-26

    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 curve's 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 20s. 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.

  13. 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

  14. 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

  15. 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.

  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. 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

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. Deformable mesh registration for the validation of automatic target localization algorithms

    PubMed Central

    Robertson, Scott; Weiss, Elisabeth; Hugo, Geoffrey D.

    2013-01-01

    Purpose: To evaluate deformable mesh registration (DMR) as a tool for validating automatic target registration algorithms used during image-guided radiation therapy. Methods: DMR was implemented in a hierarchical model, with rigid, affine, and B-spline transforms optimized in succession to register a pair of surface meshes. The gross tumor volumes (primary tumor and involved lymph nodes) were contoured by a physician on weekly CT scans in a cohort of lung cancer patients and converted to surface meshes. The meshes from weekly CT images were registered to the mesh from the planning CT, and the resulting registered meshes were compared with the delineated surfaces. Known deformations were also applied to the meshes, followed by mesh registration to recover the known deformation. Mesh registration accuracy was assessed at the mesh surface by computing the symmetric surface distance (SSD) between vertices of each registered mesh pair. Mesh registration quality in regions within 5 mm of the mesh surface was evaluated with respect to a high quality deformable image registration. Results: For 18 patients presenting with a total of 19 primary lung tumors and 24 lymph node targets, the SSD averaged 1.3 ± 0.5 and 0.8 ± 0.2 mm, respectively. Vertex registration errors (VRE) relative to the applied known deformation were 0.8 ± 0.7 and 0.2 ± 0.3 mm for the primary tumor and lymph nodes, respectively. Inside the mesh surface, corresponding average VRE ranged from 0.6 to 0.9 and 0.2 to 0.9 mm, respectively. Outside the mesh surface, average VRE ranged from 0.7 to 1.8 and 0.2 to 1.4 mm. The magnitude of errors generally increased with increasing distance away from the mesh. Conclusions: Provided that delineated surfaces are available, deformable mesh registration is an accurate and reliable method for obtaining a reference registration to validate automatic target registration algorithms for image-guided radiation therapy, specifically in regions on or near the target surfaces

  4. Error correction in image registration using POCS

    NASA Astrophysics Data System (ADS)

    Duraisamy, Prakash; Alam, Mohammad S.; Jackson, Stephen C.

    2011-04-01

    Image registration plays a vital role in many real time imaging applications. Registering the images in a precise manner is a challenging problem. In this paper, we focus on improving image registration error computation using the projection onto convex sets (POCS) techniques which improves the sub-pixel accuracy in the images leading to better estimates for the registration error. This can be used in turn to improve the registration itself. The results obtained from the proposed technique match well with the ground truth which validates the accuracy of this technique. Furthermore, the proposed technique shows better performance compared to existing methods.

  5. The role of professional education in developing compassionate practitioners: a mixed methods study exploring the perceptions xof health professionals and pre-registration students.

    PubMed

    Bray, Lucy; O'Brien, Mary R; Kirton, Jennifer; Zubairu, Kate; Christiansen, Angela

    2014-03-01

    Compassionate practice is a public expectation and a core health professional value. However, in the face of growing public and professional unease about a perceived absence of compassion in health care it is essential that the role of education in developing compassionate practitioners is fully understood. The aim of this study was to explore qualified health professionals' and pre-registration students' understanding of compassion and the role of health professional education in promoting compassionate care. A sequential explanatory mixed methods study collected data using surveys and qualitative semi-structured interviews from qualified health professionals (n=155) and pre-registration students (n=197). Participants were from a range of health and social care disciplines and registered at a UK university. The findings indicate a high level of consensus in relation to participants' understanding of compassion in health care. Acting with warmth and empathy, providing individualised patient care and acting in a way you would like others to act towards you, were seen as the most common features of compassionate care. However, ambiguities and contradictions were evident when considering the role of health professional education in promoting compassionate practice. This study adds to the debate and current understanding of the role of education in fostering compassionate health care practice.

  6. Undergraduate Cross Registration.

    ERIC Educational Resources Information Center

    Grupe, Fritz H.

    This report discusses various aspects of undergraduate cross-registration procedures, including the dimensions, values, roles and functions, basic assumptions, and facilitating and encouragment of cross-registration. Dimensions of cross-registration encompass financial exchange, eligibility, program limitations, type of grade and credit; extent of…

  7. Radar image registration and rectification

    NASA Technical Reports Server (NTRS)

    Naraghi, M.; Stromberg, W. D.

    1983-01-01

    Two techniques for radar image registration and rectification are presented. In the registration method, a general 2-D polynomial transform is defined to accomplish the geometric mapping from one image into the other. The degree and coefficients of the polynomial are obtained using an a priori found tiepoint data set. In the second part of the paper, a rectification procedure is developed that models the distortion present in the radar image in terms of the radar sensor's platform parameters and the topographic variations of the imaged scene. This model, the ephemeris data and the digital topographic data are then used in rectifying the radar image. The two techniques are then used in registering and rectifying two examples of radar imagery. Each method is discussed as to its benefits, shortcomings and registration accuracy.

  8. 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.

  9. 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.

  10. 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

  11. Deformable Image Registration with Local Rigidity Constraints for Cone-Beam CT Guided Spine Surgery

    PubMed Central

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

    2014-01-01

    Image-guided spine surgery 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 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 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. 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

  12. 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

  13. 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

  14. Novel method for rapid copper chelation assessment confirmed low affinity of D-penicillamine for copper in comparison with trientine and 8-hydroxyquinolines.

    PubMed

    Říha, Michal; Karlíčková, Jana; Filipský, Tomáš; Macáková, Kateřina; Hrdina, Radomír; Mladěnka, Přemysl

    2013-06-01

    Copper is an essential trace element involved in many physiological processes. Since disorder of copper homeostasis is observed in various pathologies, copper chelators may represent a promising therapeutic tool. This study was aimed at: 1) formation of an in vitro methodology for screening of copper chelators, and 2) detailed analysis of the interaction of copper with clinically used D-penicillamine (D-PEN), triethylenetetramine (trientine), experimentally tested 8-hydroxyquinolines, and the disodium salt of EDTA as a standard chelator. Methodology based on bathocuproinedisulfonic acid disodium salt (BCS), usable at (patho)physiologically relevant pHs (4.5-7.5), enabled assessment of both cuprous and cupric ions chelation and comparison of the relative affinities of the tested compounds for copper. In the case of potent chelators, the stoichiometry could be estimated too. Clioquinol, chloroxine and EDTA formed very stable complexes with Cu(+)/Cu(2+) at all tested pHs, while copper complexes with trientine were stable only under neutral or slightly acidic conditions. Non-substituted 8-hydroxyquinoline was a less efficient copper chelator, but still unequivocally more potent than D-PEN. Both 8-hydroxyquinoline and D-PEN chelation potencies, similarly to that of trientine, were pH-dependent and decreased with pH. Moreover, only D-PEN was able to reduce cupric ions. Conclusively, BCS assay represents a rapid, simple and precise method for copper chelation measurement. In addition, lower binding affinity of D-PEN compared with 8-hydroxyquinolines and trientine was demonstrated.

  15. Screening method of carbohydrate-binding proteins in biological sources by capillary affinity electrophoresis and its application to determination of Tulipa gesneriana agglutinin in tulip bulbs.

    PubMed

    Nakajima, Kazuki; Kinoshita, Mitsuhiro; Oda, Yasuo; Masuko, Takashi; Kaku, Hanae; Shibuya, Naoto; Kakehi, Kazuaki

    2004-09-01

    We developed capillary affinity electrophoresis (CAE) to analyze the molecular interaction between carbohydrate chains and proteins in solution state. A mixture of oligosaccharides derived from a glycoprotein was labeled with 8-aminopyrene-1,3,6-trisulfonate (APTS), and used as glycan library without isolation. Interaction of a carbohydrate-binding protein with each oligosaccharide in the mixture could be simultaneously observed, and relative affinities of oligosaccharides toward the protein were accurately determined. In this study, we applied CAE to detect the presence of lectins in some plants (Japanese elderberry bark and tulip bulb). In the crude extract of the elderberry bark, binding activity toward sialo-carbohydrate chains could be easily detected. We also examined the presence of lectins in the crude extract of tulip bulbs and determined the detailed carbohydrate-binding specificity of Tulipa gesneriana agglutinin (TGA), one of the lectins from tulip bulbs. Kinetic studies demonstrated that TGA showed novel carbohydrate-binding specificity and preferentially recognized triantennary oligosaccharides with Gal residues at nonreducing termini and a Fuc residue linked through alpha(1-6) linkage at chitobiose portion of the reducing termini but not tetraantennary carbohydrates. The results described here indicate that CAE will be a valuable method for both screening of lectins in natural sources and determination of their detailed carbohydrate-binding specificities.

  16. 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

  17. 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.

  18. 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.

  19. Automated Registration of MDIM with MOLA Tracks

    NASA Astrophysics Data System (ADS)

    Kim, J. R.; Muller, J.-P.; Morley, J. G.; Mitchell, K. L.

    2001-03-01

    We have developed a method for the automatic registration of MOLA tracks and optical images by means of a crater detection algorithm and a specialised matching function for the photogrammetric DEM creation with MOLA reference using stereo photogrammetric methods.

  20. 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.

  1. Optical flow based deformable volume registration using a novel second-order regularization prior

    NASA Astrophysics Data System (ADS)

    Grbić, Saša; Urschler, Martin; Pock, Thomas; Bischof, Horst

    2010-03-01

    Nonlinear image registration is an initial step for a large number of medical image analysis applications. Optical flow based intensity registration is often used for dealing with intra-modality applications involving motion differences. In this work we present an energy functional which uses a novel, second-order regularization prior of the displacement field. Compared to other methods our scheme is robust to non-Gaussian noise and does not penalize locally affine deformation fields in homogeneous areas. We propose an efficient and stable numerical scheme to find the minimizer of the presented energy. We implemented our algorithm using modern consumer graphics processing units and thereby increased the execution performance dramatically. We further show experimental evaluations on clinical CT thorax data sets at different breathing states and on dynamic 4D CT cardiac data sets.

  2. 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

  3. 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

  4. 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.

  5. Automatic CT-ultrasound registration for diagnostic imaging and image-guided intervention.

    PubMed

    Wein, Wolfgang; Brunke, Shelby; Khamene, Ali; Callstrom, Matthew R; Navab, Nassir

    2008-10-01

    The fusion of tracked ultrasound with CT has benefits for a variety of clinical applications, however extensive manual effort is usually required for correct registration. We developed new methods that allow one to simulate medical ultrasound from CT in real-time, reproducing the majority of ultrasonic imaging effects. They are combined with a robust similarity measure that assesses the correlation of a combination of signals extracted from CT with ultrasound, without knowing the influence of each signal. This serves as the foundation of a fully automatic registration, that aligns a 3D ultrasound sweep with the corresponding tomographic modality using a rigid or an affine transformation model, without any manual interaction. These techniques were evaluated in a study involving 25 patients with indeterminate lesions in liver and kidney. The clinical setup, acquisition and registration workflow is described, along with the evaluation of the registration accuracy with respect to physician-defined Ground Truth. Our new algorithm correctly registers without any manual interaction in 76% of the cases, the average RMS TRE over multiple target lesions throughout the liver is 8.1mm.

  6. 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.

  7. Cesium cation affinities and basicities

    NASA Astrophysics Data System (ADS)

    Gal, Jean-François; Maria, Pierre-Charles; Massi, Lionel; Mayeux, Charly; Burk, Peeter; Tammiku-Taul, Jaana

    2007-11-01

    This review focuses on the quantitative data related to cesium cation interaction with neutral or negatively charged ligands. The techniques used for measuring the cesium cation affinity (enthalpies, CCA), and cesium cation basicities (Gibbs free energies, CCB) are briefly described. The quantum chemical calculations methods that were specifically designed for the determination of cesium cation adduct structures and the energetic aspects of the interaction are discussed. The experimental results, obtained essentially from mass spectrometry techniques, and complemented by thermochemical data, are tabulated and commented. In particular, the correlations between cesium cation affinities and lithium cation affinities for the various kinds of ligands (rare gases, polyatomic neutral molecules, among them aromatic compounds and negative ions) serve as a basis for the interpretation of the diverse electrostatic modes of interaction. A brief account of some recent analytical applications of ion/molecule reactions with Cs+, as well as other cationization approaches by Cs+, is given.

  8. 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).

  9. Laser range scanning for image-guided neurosurgery: investigation of image-to-physical space registrations.

    PubMed

    Cao, Aize; Thompson, R C; Dumpuri, P; Dawant, B M; Galloway, R L; Ding, S; Miga, M I

    2008-04-01

    In this article a comprehensive set of registration methods is utilized to provide image-to-physical space registration for image-guided neurosurgery in a clinical study. Central to all methods is the use of textured point clouds as provided by laser range scanning technology. The objective is to perform a systematic comparison of registration methods that include both extracranial (skin marker point-based registration (PBR), and face-based surface registration) and intracranial methods (feature PBR, cortical vessel-contour registration, a combined geometry/intensity surface registration method, and a constrained form of that method to improve robustness). The platform facilitates the selection of discrete soft-tissue landmarks that appear on the patient's intraoperative cortical surface and the preoperative gadolinium-enhanced magnetic resonance (MR) image volume, i.e., true corresponding novel targets. In an 11 patient study, data were taken to allow statistical comparison among registration methods within the context of registration error. The results indicate that intraoperative face-based surface registration is statistically equivalent to traditional skin marker registration. The four intracranial registration methods were investigated and the results demonstrated a target registration error of 1.6 +/- 0.5 mm, 1.7 +/- 0.5 mm, 3.9 +/- 3.4 mm, and 2.0 +/- 0.9 mm, for feature PBR, cortical vessel-contour registration, unconstrained geometric/intensity registration, and constrained geometric/intensity registration, respectively. When analyzing the results on a per case basis, the constrained geometric/intensity registration performed best, followed by feature PBR, and finally cortical vessel-contour registration. Interestingly, the best target registration errors are similar to targeting errors reported using bone-implanted markers within the context of rigid targets. The experience in this study as with others is that brain shift can compromise extracranial

  10. A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands.

    PubMed

    Khandelwal, Akash; Lukacova, Viera; Comez, Dogan; Kroll, Daniel M; Raha, Soumyendu; Balaz, Stefan

    2005-08-25

    To alleviate the problems in the receptor-based design of metalloprotein ligands due to inadequacies in the force-field description of coordination bonds, a four-tier approach was devised. Representative ligand-metalloprotein interaction energies are obtained by subsequent application of (1) docking with metal-binding-guided selection of modes, (2) optimization of the ligand-metalloprotein complex geometry by combined quantum mechanics and molecular mechanics (QM/MM) methods, (3) conformational sampling of the complex with constrained metal bonds by force-field-based molecular dynamics (MD), and (4) a single point QM/MM energy calculation for the time-averaged structures. The QM/MM interaction energies are, in a linear combination with the desolvation-characterizing changes in the solvent-accessible surface areas, correlated with experimental data. The approach was applied to structural correlation of published binding free energies of a diverse set of 28 hydroxamate inhibitors to zinc-dependent matrix metalloproteinase 9 (MMP-9). Inclusion of steps 3 and 4 significantly improved both correlation and prediction. The two descriptors explained 90% of variance in inhibition constants of all 28 inhibitors, ranging from 0.08 to 349 nM, with the average unassigned error of 0.318 log units. The structural and energetic information obtained from the time-averaged MD simulation results helped understand the differences in binding modes of related compounds.

  11. Tangent height registration method for the Version 1.4 data retrieval algorithm of the solar occultation sensor ILAS-II.

    PubMed

    Tanaka, Tomoaki; Nakajima, Hideaki; Sugita, Takafumi; Ejiri, Mitsumu K; Irie, Hitoshi; Saitoh, Naoko; Terao, Yukio; Kawasaki, Hiroyuki; Usami, Masatoshi; Yokota, Tatsuya; Kobayashi, Hirokazu; Sasano, Yasuhiro

    2007-10-10

    The Improved Limb Atmospheric Spectrometer-II (ILAS-II) is a satellite-borne solar occultation sensor onboard the Advanced Earth Observing Satellite-II (ADEOS-II). The ILAS-II succeeded the ILAS. The ILAS-II used four grating spectrometers to observe vertical profiles of gas volume mixing ratios of trace constituents and was also equipped with a Sun-edge sensor to determine tangent heights geometrically with high precision. The accuracy of gas volume mixing ratios depends on the accuracy of the tangent height determination. The combination method is a tangent height registration method that was developed to give appropriate tangent heights for the ILAS-II Version 1.4 data retrieval algorithm. This study describes the method used in the ILAS-II Version 1.4 retrieval algorithm to register tangent heights. The root-sum-square total random error is estimated to be 30 m, and the total systematic error is 180 m at an altitude of 30 km. The influence of the tangent height errors on the vertical profiles of gas volume mixing ratios in ILAS-II Version 1.4 is estimated by using the relative difference. The relative difference for each species is within 7% (20%) for an altitude shift of +/-100 m(+/-300 m).

  12. Tensor scale-based image registration

    NASA Astrophysics Data System (ADS)

    Saha, Punam K.; Zhang, Hui; Udupa, Jayaram K.; Gee, James C.

    2003-05-01

    Tangible solutions to image registration are paramount in longitudinal as well as multi-modal medical imaging studies. In this paper, we introduce tensor scale - a recently developed local morphometric parameter - in rigid image registration. A tensor scale-based registration method incorporates local structure size, orientation and anisotropy into the matching criterion, and therefore, allows efficient multi-modal image registration and holds potential to overcome the effects of intensity inhomogeneity in MRI. Two classes of two-dimensional image registration methods are proposed - (1) that computes angular shift between two images by correlating their tensor scale orientation histogram, and (2) that registers two images by maximizing the similarity of tensor scale features. Results of applications of the proposed methods on proton density and T2-weighted MR brain images of (1) the same slice of the same subject, and (2) different slices of the same subject are presented. The basic superiority of tensor scale-based registration over intensity-based registration is that it may allow the use of local Gestalts formed by the intensity patterns over the image instead of simply considering intensities as isolated events at the pixel level. This would be helpful in dealing with the effects of intensity inhomogeneity and noise in MRI.

  13. 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.

  14. 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.

  15. Deformable structure registration of bladder through surface mapping.

    PubMed

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

    2006-06-01

    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

  16. 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.

  17. 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

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

    PubMed

    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.

  19. Incorporating global information in feature-based multimodal image registration

    NASA Astrophysics Data System (ADS)

    Li, Yong; Stevenson, Robert

    2014-03-01

    A multimodal image registration framework based on searching the best matched keypoints and the incorporation of global information is proposed. It comprises two key elements: keypoint detection and an iterative process. Keypoints are detected from both the reference and test images. For each test keypoint, a number of reference keypoints are chosen as mapping candidates. A triplet of keypoint mappings determine an affine transformation that is evaluated using a similarity metric between the reference image and the transformed test image by the determined transformation. An iterative process is conducted on triplets of keypoint mappings, keeping track of the best matched reference keypoint. Random sample consensus and mutual information are applied to eliminate outlier keypoint mappings. The similarity metric is defined to be the number of overlapped edge pixels over the entire images, allowing for global information to be incorporated in the evaluation of triplets of mappings. The performance of the framework is investigated with keypoints extracted by scale invariant feature transform and partial intensity invariant feature descriptor. Experimental results show that the proposed framework can provide more accurate registration than existing methods.

  20. Impact of Policy Initiatives on Civil Registration System in Haryana

    PubMed Central

    Singh, Pravin Kumar; Kaur, Manmeet; Jaswal, Nidhi; Kumar, Rajesh

    2012-01-01

    Background: Despite the existence of Registration of Birth and Death Act (1969), Civil Registration System (CRS) in India registered only 68.3% of the births and 63.2% of the deaths. Hence, National Population Policy (2000) emphasized the need to improve registration of vital events. In 2005, Haryana initiated policy changes to enhance registration of vital events. We evaluated the impact of these policy changes on CRS in 2009. Materials and Methods: Records and reports of CRS were reviewed. On the basis of the birth and deaths reported by the Sample Registration System, the proportion of births and deaths registered by CRS were estimated using the projected population from 2001 Census. Results: Before 2005, Police Stations were the registration centers in rural Haryana. On 1st January 2005, the birth and death registration was made the responsibility of Primary Health Centers (PHCs). Medical Officers at PHCs were designated as Registrar and Pharmacists as Sub-Registrar of Births and Deaths. Auxiliary Nurse Midwife and Anganwadi Workers facilitated the registration. Till 2004, the registration of births was stagnant at the level of 70% for several years, which increased to 95% by 2009. Similarly registration of death events increased from 73.5% to 92.1%. Conclusion: Haryana state is still to achieve complete registration of births and deaths, but certainly shift of registration from police to health department has strengthened the CRS. PMID:22654286

  1. 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)).

  2. 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

  3. Evaluation of the Convergence Region of an Automated Registration Method for 3D Laser Scanner Point Clouds.

    PubMed

    Bae, Kwang-Ho

    2009-01-01

    Using three dimensional point clouds from both simulated and real datasets from close and terrestrial laser scanners, the rotational and translational convergence regions of Geometric Primitive Iterative Closest Points (GP-ICP) are empirically evaluated. The results demonstrate the GP-ICP has a larger rotational convergence region than the existing methods, e.g., the Iterative Closest Point (ICP).

  4. 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

  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. 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)

  7. 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).

  8. 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.

  9. Automatic initialization for 3D bone registration

    NASA Astrophysics Data System (ADS)

    Foroughi, Pezhman; Taylor, Russell H.; Fichtinger, Gabor

    2008-03-01

    In image-guided bone surgery, sample points collected from the surface of the bone are registered to the preoperative CT model using well-known registration methods such as Iterative Closest Point (ICP). These techniques are generally very sensitive to the initial alignment of the datasets. Poor initialization significantly increases the chances of getting trapped local minima. In order to reduce the risk of local minima, the registration is manually initialized by locating the sample points close to the corresponding points on the CT model. In this paper, we present an automatic initialization method that aligns the sample points collected from the surface of pelvis with CT model of the pelvis. The main idea is to exploit a mean shape of pelvis created from a large number of CT scans as the prior knowledge to guide the initial alignment. The mean shape is constant for all registrations and facilitates the inclusion of application-specific information into the registration process. The CT model is first aligned with the mean shape using the bilateral symmetry of the pelvis and the similarity of multiple projections. The surface points collected using ultrasound are then aligned with the pelvis mean shape. This will, in turn, lead to initial alignment of the sample points with the CT model. The experiments using a dry pelvis and two cadavers show that the method can align the randomly dislocated datasets close enough for successful registration. The standard ICP has been used for final registration of datasets.

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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.

  16. 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

  17. [Analysis and discussion on current condition of acupuncture clinical research registration].

    PubMed

    Xu, Ying; Chen, Bo; Guo, Yi

    2015-06-01

    To introduce the international registration condition of acupuncture clinical research. With the examples of World Health Organization International Clinical Trials Registry Platform and the U. S. National Institutes of Health Clinical Registration Platform, the registration method and current condition of acupuncture clinical trials in international clinical trials registration platform were analyzed. The results indicate that the number of acupuncture clinical trials registration is gradually increased and the registration number from China is on the rise as well. But most domestic acupuncture clinical researches haven't been registered arid the researchers' valuing degree for clinical trials registration and methodology research needs to be improved. PMID:26480568

  18. 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

  19. 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

  20. Designing Chaotic Systems by Piecewise Affine Systems

    NASA Astrophysics Data System (ADS)

    Wu, Tiantian; Li, Qingdu; Yang, Xiao-Song

    Based on mathematical analysis, this paper provides a methodology to ensure the existence of homoclinic orbits in a class of three-dimensional piecewise affine systems. In addition, two chaotic generators are provided to illustrate the effectiveness of the method.

  1. 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.

  2. 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.

  3. 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.

  4. A complementary method to CD4 counting: measurement of CD4+/CD8+ T lymphocyte ratio in a tandem affinity microfluidic system.

    PubMed

    Li, Wenjie; Gao, Yan; Pappas, Dimitri

    2015-12-01

    We describe a tandem affinity microfluidic separation that measures the ratio of CD4+/CD8+ T lymphocytes from blood samples. It is performed by injecting 2 μL of lysed blood samples at 1800-2700 cells μL(-1) into a microfluidic device containing two serially linked affinity regions, followed with a stop flow incubation that captures CD4+/CD8+ T lymphocytes on the corresponding affinity regions. Fluorophore conjugated antibodies are then injected at a controlled shear stress of 1.7 dyn cm(-2) to label target cells while eluting non-specific cells; and at last the CD4/CD8 ratio is calculated after the cell enumeration. The ratio of CD4+/CD8+ T lymphocytes achieved by our tandem affinity microfluidic system was in close agreement with that performed using conventional flow cytometry (R (2)  = 0.97) over a wide range (0.4-2.5) that covered the reference values from immune deficient patients to healthy people. This approach may represent an inexpensive and powerful tool in diagnosis of immunodeficiency disorders including HIV or mycobacterium tuberculosis.

  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. 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,...

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. Registration of 3D fetal neurosonography and MRI☆

    PubMed Central

    Kuklisova-Murgasova, Maria; Cifor, Amalia; Napolitano, Raffaele; Papageorghiou, Aris; Quaghebeur, Gerardine; Rutherford, Mary A.; Hajnal, Joseph V.; Noble, J. Alison; Schnabel, Julia A.

    2013-01-01

    We propose a method for registration of 3D fetal brain ultrasound with a reconstructed magnetic resonance fetal brain volume. This method, for the first time, allows the alignment of models of the fetal brain built from magnetic resonance images with 3D fetal brain ultrasound, opening possibilities to develop new, prior information based image analysis methods for 3D fetal neurosonography. The reconstructed magnetic resonance volume is first segmented using a probabilistic atlas and a pseudo ultrasound image volume is simulated from the segmentation. This pseudo ultrasound image is then affinely aligned with clinical ultrasound fetal brain volumes using a robust block-matching approach that can deal with intensity artefacts and missing features in the ultrasound images. A qualitative and quantitative evaluation demonstrates good performance of the method for our application, in comparison with other tested approaches. The intensity average of 27 ultrasound images co-aligned with the pseudo ultrasound template shows good correlation with anatomy of the fetal brain as seen in the reconstructed magnetic resonance image. PMID:23969169

  16. Curvelet-based registration of multi-component seismic waves

    NASA Astrophysics Data System (ADS)

    Wang, Hairong; Cheng, Yuanfeng; Ma, Jianwei

    2014-05-01

    Registration of the travel time of PP waves and PS waves on the same coordinate is critical for joint interpretation in multi-component seismic exploration. In this paper, we propose a new curvelet-based registration method to improve the precision of registration, especially for the data with heavy random noises. By making registration in curvelet multiscale spaces from coarser to finer scale, the proposed method is not sensitive to initial values of velocity ratio of PP waves and PS waves. Applications of the new method to real seismic dataset from Shengli Oilfield, China show good registered results in terms of both qualitative and quantitative analysis, in comparison with a traditional registration method and a wavelet-based method.

  17. 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…

  18. 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…

  19. A reproducible evaluation of ANTs similarity metric performance in brain image registration.

    PubMed

    Avants, Brian B; Tustison, Nicholas J; Song, Gang; Cook, Philip A; Klein, Arno; Gee, James C

    2011-02-01

    The United States National Institutes of Health (NIH) commit significant support to open-source data and software resources in order to foment reproducibility in the biomedical imaging sciences. Here, we report and evaluate a recent product of this commitment: Advanced Neuroimaging Tools (ANTs), which is approaching its 2.0 release. The ANTs open source software library consists of a suite of state-of-the-art image registration, segmentation and template building tools for quantitative morphometric analysis. In this work, we use ANTs to quantify, for the first time, the impact of similarity metrics on the affine and deformable components of a template-based normalization study. We detail the ANTs implementation of three similarity metrics: squared intensity difference, a new and faster cross-correlation, and voxel-wise mutual information. We then use two-fold cross-validation to compare their performance on openly available, manually labeled, T1-weighted MRI brain image data of 40 subjects (UCLA's LPBA40 dataset). We report evaluation results on cortical and whole brain labels for both the affine and deformable components of the registration. Results indicate that the best ANTs methods are competitive with existing brain extraction results (Jaccard=0.958) and cortical labeling approaches. Mutual information affine mapping combined with cross-correlation diffeomorphic mapping gave the best cortical labeling results (Jaccard=0.669±0.022). Furthermore, our two-fold cross-validation allows us to quantify the similarity of templates derived from different subgroups. Our open code, data and evaluation scripts set performance benchmark parameters for this state-of-the-art toolkit. This is the first study to use a consistent transformation framework to provide a reproducible evaluation of the isolated effect of the similarity metric on optimal template construction and brain labeling.

  20. DTI Image Registration under Probabilistic Fiber Bundles Tractography Learning

    PubMed Central

    Lei, Tao; Fan, Yangyu; Zhang, Xiuwei

    2016-01-01

    Diffusion Tensor Imaging (DTI) image registration is an essential step for diffusion tensor image analysis. Most of the fiber bundle based registration algorithms use deterministic fiber tracking technique to get the white matter fiber bundles, which will be affected by the noise and volume. In order to overcome the above problem, we proposed a Diffusion Tensor Imaging image registration method under probabilistic fiber bundles tractography learning. Probabilistic tractography technique can more reasonably trace to the structure of the nerve fibers. The residual error estimation step in active sample selection learning is improved by modifying the residual error model using finite sample set. The calculated deformation field is then registered on the DTI images. The results of our proposed registration method are compared with 6 state-of-the-art DTI image registration methods under visualization and 3 quantitative evaluation standards. The experimental results show that our proposed method has a good comprehensive performance. PMID:27774455

  1. 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.

  2. Measuring an antibody affinity distribution molecule by molecule.

    PubMed

    Temirov, Jamshid P; Bradbury, Andrew R M; Werner, James H

    2008-11-15

    Single molecule fluorescence microscopy was used to observe the binding and unbinding of hapten decorated quantum dots to 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.

  3. 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.

  4. Affinity driven social networks

    NASA Astrophysics Data System (ADS)

    Ruyú, B.; Kuperman, M. N.

    2007-04-01

    In this work we present a model for evolving networks, where the driven force is related to the social affinity between individuals of a population. In the model, a set of individuals initially arranged on a regular ordered network and thus linked with their closest neighbors are allowed to rearrange their connections according to a dynamics closely related to that of the stable marriage problem. We show that the behavior of some topological properties of the resulting networks follows a non trivial pattern.

  5. Data organization and storage model of the realty uniform registration system

    NASA Astrophysics Data System (ADS)

    Shen, Chenhua; Liu, Yu; Wu, Xiaobin

    2007-06-01

    Based on the Real Right Law, this article analyzes the entity objects of the realty uniform registration, and establishes the model of the logical relations among the entities, from which the dada relation model is proposed, and from which the data relation model of the realty uniform registration is proposed, and is compared with the current land registration data model and the real estate data model. It is proved that this uniform registration data model has not only maintained the close links with the land registration data model and the real estate registration data model, but also met the need of the uniform registration by comparing with the existing land registration data model and the real estate data model. In the end, this article discusses the method of data storage for the uniform registration of the land and the real estate to improve the efficiency of storage and access by adopting split technology to store the alteration data logically.

  6. 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

  7. 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.

  8. Large deformation diffeomorphic registration of diffusion-weighted imaging data

    PubMed Central

    Zhang, Pei; Niethammer, Marc; Shen, Dinggang; Yap, Pew-Thian

    2014-01-01

    Registration plays an important role in group analysis of diffusion-weighted imaging (DWI) data. It can be used to build a reference anatomy for investigating structural variation or tracking changes in white matter. Unlike traditional scalar image registration where spatial alignment is the only focus, registration of DWI data requires both spatial alignment of structures and reorientation of local signal profiles. As such, DWI registration is much more complex and challenging than scalar image registration. Although a variety of algorithms has been proposed to tackle the problem, most of them are restricted by the zdiffusion model used for registration, making it difficult to fit to the registered data a different model. In this paper we describe a method that allows any diffusion model to be fitted after registration for subsequent multifaceted analysis. This is achieved by directly aligning DWI data using a large deformation diffeomorphic registration framework. Our algorithm seeks the optimal coordinate mapping by simultaneously considering structural alignment, local signal profile reorientation, and deformation regularization. Our algorithm also incorporates a multi-kernel strategy to concurrently register anatomical structures at different scales. We demonstrate the efficacy of our approach using in vivo data and report detailed qualitative and quantitative results in comparison with several different registration strategies. PMID:25106710

  9. Registration of large data sets for multimodal inspection

    NASA Astrophysics Data System (ADS)

    Vedula, Venumadhav V. S.; Sheri, George

    2006-08-01

    Registration plays a key role in multimodal data fusion to extract synergistic information from multiple non-destructive evaluation (NDE) sources. One of the common techniques for registration of point datasets is the Iterative Closest Point (ICP) Algorithm. Generally, modern day NDE techniques generate large datasets and conventional ICP algorithm requires huge amount of time to register datasets to the desired accuracy. In this paper, we present algorithms to aid in the registration of large 3D NDE data sets in less time with the required accuracy. Various methods of coarse registration of data, partial registration and data reduction are used to realize this. These techniques have been used in registration and it is shown that registration can be accomplished to the desired accuracy with more than 90% reduction in time as compared to conventional ICP algorithm. Volumes of interest (VOI) can be defined on the data sets and merged together so that only the features of interest are used in the registration. The proposed algorithm also provides capability for eliminating noise in the data sets. Registration of Computed Tomography (CT) Image data, Coordinate Measuring Machine (CMM) Inspection data and CAD model has been discussed in the present work. The algorithm is generic in nature and can be applied to any other NDE inspection data.

  10. 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.

  11. 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

  12. 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.

  13. Registration of dynamic contrast-enhanced MRI using a progressive principal component registration (PPCR)

    NASA Astrophysics Data System (ADS)

    Melbourne, A.; Atkinson, D.; White, M. J.; Collins, D.; Leach, M.; Hawkes, D.

    2007-09-01

    Registration of dynamic contrast-enhanced magnetic resonance images (DCE-MRI) of soft tissue is difficult. Conventional registration cost functions that depend on information content are compromised by the changing intensity profile, leading to misregistration. We present a new data-driven model of uptake patterns formed from a principal components analysis (PCA) of time-series data, avoiding the need for a physiological model. We term this process progressive principal component registration (PPCR). Registration is performed repeatedly to an artificial time series of target images generated using the principal components of the current best-registered time-series data. The aim is to produce a dataset that has had random motion artefacts removed but long-term contrast enhancement implicitly preserved. The procedure is tested on 22 DCE-MRI datasets of the liver. Preliminary assessment of the images is by expert observer comparison with registration to the first image in the sequence. The PPCR is preferred in all cases where a preference exists. The method requires neither segmentation nor a pharmacokinetic uptake model and can allow successful registration in the presence of contrast enhancement.

  14. 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

  15. 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.

  16. Negative homotropic cooperativity and affinity heterogeneity: preparation of yeast glyceraldehyde-3-phosphate dehydrogenase with maximal affinity homogeneity.

    PubMed Central

    Gennis, L S

    1976-01-01

    A three-step procedure including affinity chromatography on NAD+-azobenzamidopropyl-Sepharose has been designed for the purification of yeast glyceraldehyde-3-phosphate dehydrogenase [D-glyceraldehyde-3-phosphate: NAD+ oxidoreductase (phosphorylating), EC 1.2.1.12] with maximized specific activity and maximized homogeneity with respect to affinity for the coenzyme, NAD+.Binding isotherms allow the analysis of cooperativity patterns that disclose both the average ligand affinity in the system and the distribution of ligands among the sites, only for systems with complete affinity homogeneity. The presence of affinity heterogeneity, resulting from multiple oligomeric species differing only in their affinity for coenzyme, gives rise to isotherms which falsely manifest apparent negative cooperativity. A method for distinguishing negative homotropic cooperativity from affinity heterogeneity is suggested. PMID:186779

  17. 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.

  18. 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.

  19. HAMS: High-Affinity Mass Spectrometry Screening. A High-Throughput Screening Method for Identifying the Tightest-Binding Lead Compounds for Target Proteins with No False Positive Identifications

    NASA Astrophysics Data System (ADS)

    Imaduwage, Kasun P.; Go, Eden P.; Zhu, Zhikai; Desaire, Heather

    2016-09-01

    A major challenge in drug discovery is the identification of high affinity lead compounds that bind a particular target protein; these leads are typically identified by high throughput screens. Mass spectrometry has become a detection method of choice in drug screening assays because the target and the ligand need not be modified. Label-free assays are advantageous because they can be developed more rapidly than assays requiring labels, and they eliminate the risk of the label interfering with the binding event. However, in commonly used MS-based screening methods, detection of false positives is a major challenge. Here, we describe a detection strategy designed to eliminate false positives. In this approach, the protein and the ligands are incubated together, and the non-binders are separated for detection. Hits (protein binders) are not detectable by MS after incubation with the protein, but readily identifiable by MS when the target protein is not present in the incubation media. The assay was demonstrated using three different proteins and hundreds of non-inhibitors; no false positive hits were identified in any experiment. The assay can be tuned to select for ligands of a particular binding affinity by varying the quantity of protein used and the immobilization method. As examples, the method selectively detected inhibitors that have Ki values of 0.2 μM, 50 pM, and 700 pM. These findings demonstrate that the approach described here compares favorably with traditional MS-based screening methods.

  20. HAMS: High-Affinity Mass Spectrometry Screening. A High-Throughput Screening Method for Identifying the Tightest-Binding Lead Compounds for Target Proteins with No False Positive Identifications

    NASA Astrophysics Data System (ADS)

    Imaduwage, Kasun P.; Go, Eden P.; Zhu, Zhikai; Desaire, Heather

    2016-11-01

    A major challenge in drug discovery is the identification of high affinity lead compounds that bind a particular target protein; these leads are typically identified by high throughput screens. Mass spectrometry has become a detection method of choice in drug screening assays because the target and the ligand need not be modified. Label-free assays are advantageous because they can be developed more rapidly than assays requiring labels, and they eliminate the risk of the label interfering with the binding event. However, in commonly used MS-based screening methods, detection of false positives is a major challenge. Here, we describe a detection strategy designed to eliminate false positives. In this approach, the protein and the ligands are incubated together, and the non-binders are separated for detection. Hits (protein binders) are not detectable by MS after incubation with the protein, but readily identifiable by MS when the target protein is not present in the incubation media. The assay was demonstrated using three different proteins and hundreds of non-inhibitors; no false positive hits were identified in any experiment. The assay can be tuned to select for ligands of a particular binding affinity by varying the quantity of protein used and the immobilization method. As examples, the method selectively detected inhibitors that have Ki values of 0.2 μM, 50 pM, and 700 pM. These findings demonstrate that the approach described here compares favorably with traditional MS-based screening methods.

  1. REGISTRATION OF ORTHODONTIC DIGITAL MODELS

    PubMed Central

    Grauer, Dan; Cevidanes, Lucia H.; Tyndall, Donald; Styner, Martin A.; Flood, Patrick M.; Proffit, William R.

    2011-01-01

    Current methods to assess outcomes and change in orthodontics are comparison of photographs, cephalometric measurements and superimpositions, and comparisons/measurements on dental casts. Digital models are a relatively new records modality in orthodontics. They offer numerous advantages in terms of storage space, spatial registration and superimposition. The purpose of this chapter is to determine the reproducibility of: 1) establishing occlusion of independently scanned digital models; and 2) registering digital models obtained after treatment on their homologous digital model setups produced before treatment. Reliability of both procedures was assessed with two random samples of five patient’s models. In both experiments, three replicate positionings of the models per patient were created and variability in position was evaluated by the maximum surface difference between replicates, and the standard deviation of the surface distances between replicates respectively. Based on the data obtained, we concluded that it is reliable to register independently scanned models to a scanned surface of the models in occlusion. Surface-to-surface registration of final orthodontic digital models to planned setup models also is reproducible. PMID:26549917

  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.

  3. 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

  4. 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.

  5. 76 FR 79173 - Registration Review; Pesticide Dockets Opened for Review and Comment, and Notice of Availability...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-21

    ...: Notice. SUMMARY: EPA has established registration review dockets for the pesticides listed in the table... reviews. Registration review is EPA's periodic review of pesticide registrations to ensure that each... interest provided in the table in Unit III.A., by one of the following methods: Federal eRulemaking...

  6. 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.

  7. 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

  8. 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.

  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. 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.

  11. A statistical framework for inter-group image registration.

    PubMed

    Liao, Shu; Wu, Guorong; Shen, Dinggang

    2012-10-01

    Groupwise image registration plays an important role in medical image analysis. The principle of groupwise image registration is to align a given set of images to a hidden template space in an iteratively manner without explicitly selecting any individual image as the template. Although many approaches have been proposed to address the groupwise image registration problem for registering a single group of images, few attentions and efforts have been paid to the registration problem between two or more different groups of images. In this paper, we propose a statistical framework to address the registration problems between two different image groups. The main contributions of this paper lie in the following aspects: (1) In this paper, we demonstrate that directly registering the group mean images estimated from two different image groups is not sufficient to establish the reliable transformation from one image group to the other image group. (2) A novel statistical framework is proposed to extract anatomical features from the white matter, gray matter and cerebrospinal fluid tissue maps of all aligned images as morphological signatures for each voxel. The extracted features provide much richer anatomical information than the voxel intensity of the group mean image, and can be integrated with the multi-channel Demons registration algorithm to perform the registration process. (3) The proposed method has been extensively evaluated on two publicly available brain MRI databases: the LONI LPBA40 and the IXI databases, and it is also compared with a conventional inter-group image registration approach which directly performs deformable registration between the group mean images of two image groups. Experimental results show that the proposed method consistently achieves higher registration accuracy than the method under comparison.

  12. Informing pre-registration nurse education: a proposal outline on the value, methods and ethical considerations of involving children in doctoral research.

    PubMed

    Clarke, Sonya

    2014-12-01

    As pre-registration nurse education programmes evolve within the United Kingdom, it is imperative to involve patient/client groups within the research process, as the outcome may invoke a change in the care delivery of the registered nurse (RN). This paper focuses upon children and how children might hypothetically contribute to informing a generic nursing programme in their capacity as a rights holder and expert in their own lives. Even though their contribution and value has been debated around their capacity as research advisor, research participant and co researcher, this paper explores how the child's view of their experience of hospital and of the good nurse could be best captured. Research is a powerful vehicle that can enable their voice to equally inform UK nurse educators and policy makers so that the child's health care needs are effectively met in hospital by RN's who complete a generic programme.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. The adaptive FEM elastic model for medical image registration.

    PubMed

    Zhang, Jingya; Wang, Jiajun; Wang, Xiuying; Feng, Dagan

    2014-01-01

    This paper proposes an adaptive mesh refinement strategy for the finite element method (FEM) based elastic registration model. The signature matrix for mesh refinement takes into account the regional intensity variance and the local deformation displacement. The regional intensity variance reflects detailed information for improving registration accuracy and the deformation displacement fine-tunes the mesh refinement for a more efficient algorithm. The gradient flows of two different similarity metrics, the sum of the squared difference and the spatially encoded mutual information for the mono-modal and multi-modal registrations, are used to derive external forces to drive the model to the equilibrium state. We compared our approach to three other models: (1) the conventional multi-resolution FEM registration algorithm; (2) the FEM elastic method that uses variation information for mesh refinement; and (3) the robust block matching based registration. Comparisons among different methods in a dataset with 20 CT image pairs upon artificial deformation demonstrate that our registration method achieved significant improvement in accuracies. Experimental results in another dataset of 40 real medical image pairs for both mono-modal and multi-modal registrations also show that our model outperforms the other three models in its accuracy.

  18. 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.

  19. 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

  20. Proton affinities of hydrated molecules

    NASA Astrophysics Data System (ADS)

    Valadbeigi, Younes

    2016-09-01

    Proton affinities (PA) of non-hydrated, M, and hydrated forms, M(H2O)1,2,3, of 20 organic molecules including alcohols, ethers, aldehydes, ketones and amines were calculated by the B3LYP/6-311++G(d,p) method. For homogeneous families, linear correlations were observed between PAs of the M(H2O)1,2,3 and the PAs of the non-hydrated molecules. Also, the absolute values of the hydration enthalpies of the protonated molecules decreased linearly with the PAs. The correlation functions predicted that for an amine with PA < 1100 kJ/mol the PA(M(H2O)) is larger than the corresponding PA, while for an amine with PA > 1100 kJ/mol the PA(M(H2O)) is smaller than the PA.

  1. 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).

  2. Affine Invariant Character Recognition by Progressive Removing

    NASA Astrophysics Data System (ADS)

    Iwamura, Masakazu; Horimatsu, Akira; Niwa, Ryo; Kise, Koichi; Uchida, Seiichi; Omachi, Shinichiro

    Recognizing characters in scene images suffering from perspective distortion is a challenge. Although there are some methods to overcome this difficulty, they are time-consuming. In this paper, we propose a set of affine invariant features and a new recognition scheme called “progressive removing” that can help reduce the processing time. Progressive removing gradually removes less feasible categories and skew angles by using multiple classifiers. We observed that progressive removing and the use of the affine invariant features reduced the processing time by about 60% in comparison to a trivial one without decreasing the recognition rate.

  3. Robust Point Set Registration Using Gaussian Mixture Models.

    PubMed

    Jian, Bing; Vemuri, Baba C

    2011-08-01

    In this paper, we present a unified framework for the rigid and nonrigid point set registration problem in the presence of significant amounts of noise and outliers. The key idea of this registration framework is to represent the input point sets using Gaussian mixture models. Then, the problem of point set registration is reformulated as the problem of aligning two Gaussian mixtures such that a statistical discrepancy measure between the two corresponding mixtures is minimized. We show that the popular iterative closest point (ICP) method [1] and several existing point set registration methods [2], [3], [4], [5], [6], [7] in the field are closely related and can be reinterpreted meaningfully in our general framework. Our instantiation of this general framework is based on the the L2 distance between two Gaussian mixtures, which has the closed-form expression and in turn leads to a computationally efficient registration algorithm. The resulting registration algorithm exhibits inherent statistical robustness, has an intuitive interpretation, and is simple to implement. We also provide theoretical and experimental comparisons with other robust methods for point set registration. PMID:21173443

  4. European and international collaboration in affinity proteomics.

    PubMed

    Stoevesandt, Oda; Taussig, Michael J

    2012-06-15

    In affinity proteomics, specific protein-binding molecules (a.k.a. binders), principally antibodies, are applied as reagents in proteome analysis. In recent years, advances in binder technologies have created the potential for an unprecedented view on protein expression and distribution patterns in plasma, cells and tissues and increasingly on protein function. Particular strengths of affinity proteomics methods include detecting proteins in their natural environments of cell or tissue, high sensitivity and selectivity for detection of low abundance proteins and exploiting binding actions such as functional interference in living cells. To maximise the use and impact of affinity reagents, it will be essential to create comprehensive, standardised binder collections. With this in mind, the EU FP7 programme AFFINOMICS (http://www.affinomics.org), together with the preceding EU programmes ProteomeBinders and AffinityProteome, aims to extend affinity proteomics research by generating a large-scale resource of validated protein-binding molecules for characterisation of the human proteome. Activity is directed at producing binders to about 1000 protein targets, primarily in signal transduction and cancer, by establishing a high throughput, coordinated production pipeline. An important aspect of AFFINOMICS is the development of highly efficient recombinant selection methods, based on phage, cell and ribosome display, capable of producing high quality binders at greater throughput and lower cost than hitherto. The programme also involves development of innovative and sensitive technologies for specific detection of target proteins and their interactions, and deployment of binders in proteomics studies of clinical relevance. The need for such binder generation programmes is now recognised internationally, with parallel initiatives in the USA for cancer (NCI) and transcription factors (NIH) and within the Human Proteome Organisation (HUPO). The papers in this volume of New

  5. 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.

  6. Affinity chromatography for purification of two urokinases from human urine.

    PubMed

    Takahashi, R; Akiba, K; Koike, M; Noguchi, T; Ezure, Y

    2000-05-26

    A new affinity chromatography (hydrophobic-mediated affinity chromatography), which was characterized by the matrix having both affinity site to urokinase and hydrophobic site, was established for the purification of urokinase from human urine. The hydrophobic affinity matrix (tentatively named PAS in the text) was prepared by immobilizing 6-aminocaproic acid on Sepharose CL-6B, followed by a coupling p-aminobenzamidine to a part of the hydrophobic site on the matrix. The PAS matrix was applied to the purification of urokinase from human urine, and high- and low-molecular weight pure urokinases were efficiently obtained in high yield by the present method. PMID:10892585

  7. Rapid registration of multimodal images using a reduced number of voxels

    NASA Astrophysics Data System (ADS)

    Huang, Xishi; Hill, Nicholas A.; Ren, Jing; Peters, Terry M.

    2006-03-01

    Rapid registration of multimodal cardiac images can improve image-guided cardiac surgeries and cardiac disease diagnosis. While mutual information (MI) is arguably the most suitable registration technique, this method is too slow to converge for real time cardiac image registration; moreover, correct registration may not coincide with a global or even local maximum of MI. These limitations become quite evident when registering three-dimensional (3D) ultrasound (US) images and dynamic 3D magnetic resonance (MR) images of the beating heart. To overcome these issues, we present a registration method that uses a reduced number of voxels, while retaining adequate registration accuracy. Prior to registration we preprocess the images such that only the most representative anatomical features are depicted. By selecting samples from preprocessed images, our method dramatically speeds up the registration process, as well as ensuring correct registration. We validated this registration method for registering dynamic US and MR images of the beating heart of a volunteer. Experimental results on in vivo cardiac images demonstrate significant improvements in registration speed without compromising registration accuracy. A second validation study was performed registering US and computed tomography (CT) images of a rib cage phantom. Two similarity metrics, MI and normalized crosscorrelation (NCC) were used to register the image sets. Experimental results on the rib cage phantom indicate that our method can achieve adequate registration accuracy within 10% of the computation time of conventional registration methods. We believe this method has the potential to facilitate intra-operative image fusion for minimally invasive cardio-thoracic surgical navigation.

  8. 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.

  9. 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.

  10. A new combined surface and volume registration

    NASA Astrophysics Data System (ADS)

    Lepore, Natasha; Joshi, Anand A.; Leahy, Richard M.; Brun, Caroline; Chou, Yi-Yu; Pennec, Xavier; Lee, Agatha D.; Barysheva, Marina; De Zubicaray, Greig I.; Wright, Margaret J.; McMahon, Katie L.; Toga, Arthur W.; Thompson, Paul M.

    2010-03-01

    3D registration of brain MRI data is vital for many medical imaging applications. However, purely intensitybased approaches for inter-subject matching of brain structure are generally inaccurate in cortical regions, due to the highly complex network of sulci and gyri, which vary widely across subjects. Here we combine a surfacebased cortical registration with a 3D fluid one for the first time, enabling precise matching of cortical folds, but allowing large deformations in the enclosed brain volume, which guarantee diffeomorphisms. This greatly improves the matching of anatomy in cortical areas. The cortices are segmented and registered with the software Freesurfer. The deformation field is initially extended to the full 3D brain volume using a 3D harmonic mapping that preserves the matching between cortical surfaces. Finally, these deformation fields are used to initialize a 3D Riemannian fluid registration algorithm, that improves the alignment of subcortical brain regions. We validate this method on an MRI dataset from 92 healthy adult twins. Results are compared to those based on volumetric registration without surface constraints; the resulting mean templates resolve consistent anatomical features both subcortically and at the cortex, suggesting that the approach is well-suited for cross-subject integration of functional and anatomic data.

  11. Automated robust registration of grossly misregistered whole-slide images with varying stains

    NASA Astrophysics Data System (ADS)

    Litjens, G.; Safferling, K.; Grabe, N.

    2016-03-01

    Cancer diagnosis and pharmaceutical research increasingly depend on the accurate quantification of cancer biomarkers. Identification of biomarkers is usually performed through immunohistochemical staining of cancer sections on glass slides. However, combination of multiple biomarkers from a wide variety of immunohistochemically stained slides is a tedious process in traditional histopathology due to the switching of glass slides and re-identification of regions of interest by pathologists. Digital pathology now allows us to apply image registration algorithms to digitized whole-slides to align the differing immunohistochemical stains automatically. However, registration algorithms need to be robust to changes in color due to differing stains and severe changes in tissue content between slides. In this work we developed a robust registration methodology to allow for fast coarse alignment of multiple immunohistochemical stains to the base hematyoxylin and eosin stained image. We applied HSD color model conversion to obtain a less stain color dependent representation of the whole-slide images. Subsequently, optical density thresholding and connected component analysis were used to identify the relevant regions for registration. Template matching using normalized mutual information was applied to provide initial translation and rotation parameters, after which a cost function-driven affine registration was performed. The algorithm was validated using 40 slides from 10 prostate cancer patients, with landmark registration error as a metric. Median landmark registration error was around 180 microns, which indicates performance is adequate for practical application. None of the registrations failed, indicating the robustness of the algorithm.

  12. 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.

  13. 22 CFR 122.3 - Registration fees.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... reviewed, adjudicated or issued a response. The additional fee will be determined by multiplying $250 times...) Lapse in registration. A registrant who fails to renew a registration and, after an intervening...

  14. 22 CFR 122.3 - Registration fees.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... reviewed, adjudicated or issued a response. The additional fee will be determined by multiplying $250 times...) Lapse in registration. A registrant who fails to renew a registration and, after an intervening...

  15. 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)

  16. 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

  17. Spatially adaptive log-euclidean polyaffine registration based on sparse matches.

    PubMed

    Taquet, Maxime; Macq, Benoît; Warfield, Simon K

    2011-01-01

    Log-euclidean polyaffine transforms have recently been introduced to characterize the local affine behavior of the deformation in principal anatomical structures. The elegant mathematical framework makes them a powerful tool for image registration. However, their application is limited to large structures since they require the pre-definition of affine regions. This paper extends the polyaffine registration to adaptively fit a log-euclidean polyaffine transform that captures deformations at smaller scales. The approach is based on the sparse selection of matching points in the images and the formulation of the problem as an expectation maximization iterative closest point problem. The efficiency of the algorithm is shown through experiments on inter-subject registration of brain MRI between a healthy subject and patients with multiple sclerosis.

  18. 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.

  19. 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

  20. Automated image registration for FDOPA PET studies

    NASA Astrophysics Data System (ADS)

    Lin, Kang-Ping; Huang, Sung-Cheng; Yu, Dan-Chu; Melega, William; Barrio, Jorge R.; Phelps, Michael E.

    1996-12-01

    In this study, various image registration methods are investigated for their suitability for registration of L-6-[18F]-fluoro-DOPA (FDOPA) PET images. Five different optimization criteria including sum of absolute difference (SAD), mean square difference (MSD), cross-correlation coefficient (CC), standard deviation of pixel ratio (SDPR), and stochastic sign change (SSC) were implemented and Powell's algorithm was used to optimize the criteria. The optimization criteria were calculated either unidirectionally (i.e. only evaluating the criteria for comparing the resliced image 1 with the original image 2) or bidirectionally (i.e. averaging the criteria for comparing the resliced image 1 with the original image 2 and those for the sliced image 2 with the original image 1). Monkey FDOPA images taken at various known orientations were used to evaluate the accuracy of different methods. A set of human FDOPA dynamic images was used to investigate the ability of the methods for correcting subject movement. It was found that a large improvement in performance resulted when bidirectional rather than unidirectional criteria were used. Overall, the SAD, MSD and SDPR methods were found to be comparable in performance and were suitable for registering FDOPA images. The MSD method gave more adequate results for frame-to-frame image registration for correcting subject movement during a dynamic FDOPA study. The utility of the registration method is further demonstrated by registering FDOPA images in monkeys before and after amphetamine injection to reveal more clearly the changes in spatial distribution of FDOPA due to the drug intervention.

  1. 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.

  2. 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

  3. INTER-GROUP IMAGE REGISTRATION BY HIERARCHICAL GRAPH SHRINKAGE.

    PubMed

    Ying, Shihui; Wu, Guorong; Liao, Shu; Shen, Dinggang

    2013-12-31

    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.

  4. 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

  5. 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

  6. 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

  7. 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.'

  8. 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.

  9. Permeability of self-affine rough fractures

    PubMed

    Drazer; Koplik

    2000-12-01

    The permeability of two-dimensional fractures with self-affine fractal roughness is studied via analytic arguments and numerical simulations. The limit where the roughness amplitude is small compared with average fracture aperture is analyzed by a perturbation method, while in the opposite case of narrow aperture, we use heuristic arguments based on lubrication theory. Numerical simulations, using the lattice Boltzmann method, are used to examine the complete range of aperture sizes, and confirm the analytic arguments. PMID:11138092

  10. 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.

  11. 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.

  12. Proton affinities and photoelectron spectra of phenylalanine and N-methyl- and N,N-dimethylphenylalanine. Correlation of lone pair ionization energies with proton affinities and implications for N-methylation as a method to effect site specific protonation of peptides

    SciTech Connect

    Campbell, S.; Marzluff, E.M.; Rodgers, M.T.; Beauchamp, J.L. ); Rempe, M.E.; Schwinck, K.F.; Lichtenberger, D.L. )

    1994-06-15

    A Fourier transform ion cyclotron resonance (FT-ICR) technique for measuring gas-phase proton affinities is presented which utilizes collisional dissociation of proton-bound clusters by off-resonance translational excitation. A simplified RRKM analysis relates unimolecular dissociation rates to proton affinities. This technique is used to measure values for the proton affinities of phenylalanine and N-methyl- and N,N-dimethylphenylalanine of 220.3, 223.6, and 224.5 kcal/mol, respectively (relative to the proton affinity of NH[sub 3] = 204.0 kcal/mol). The proton affinity measured for phenylalanine is in excellent agreement with reported literature values. The photoelectron spectra of these three molecules are also presented and analyzed. Assignments of bands to specific ionization processes are aided by comparison with model compounds such as methyl-substituted amines and 2-phenylethylamines. These data are employed to examine the correlation of adiabatic nitrogen lone pair ionization energies with gas-phase proton affinities for phenylalanine, N-methylphenylalanine, and N,N-dimethylphenylalanine in comparison to correlations for other amino acids and selected aliphatic amines. 41 refs., 7 figs., 2 tabs.

  13. 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.

  14. An Iterative Image Registration Algorithm by Optimizing Similarity Measurement.

    PubMed

    Chu, Wei; Ma, Li; Song, John; Vorburger, Theodore

    2010-01-01

    A new registration algorithm based on Newton-Raphson iteration is proposed to align images with rigid body transformation. A set of transformation parameters consisting of translation in x and y and rotation angle around z is calculated by optimizing a specified similarity metric using the Newton-Raphson method. This algorithm has been tested by registering and correlating pairs of topography measurements of nominally identical NIST Standard Reference Material (SRM 2461) standard cartridge cases, and very good registration accuracy has been obtained.

  15. Modern affinity reagents: Recombinant antibodies and aptamers.

    PubMed

    Groff, Katherine; Brown, Jeffrey; Clippinger, Amy J

    2015-12-01

    Affinity reagents are essential tools in both basic and applied research; however, there is a growing concern about the reproducibility of animal-derived monoclonal antibodies. The need for higher quality affinity reagents has prompted the development of methods that provide scientific, economic, and time-saving advantages and do not require the use of animals. This review describes two types of affinity reagents, recombinant antibodies and aptamers, which are non-animal technologies that can replace the use of animal-derived monoclonal antibodies. Recombinant antibodies are protein-based reagents, while aptamers are nucleic-acid-based. In light of the scientific advantages of these technologies, this review also discusses ways to gain momentum in the use of modern affinity reagents, including an update to the 1999 National Academy of Sciences monoclonal antibody production report and federal incentives for recombinant antibody and aptamer efforts. In the long-term, these efforts have the potential to improve the overall quality and decrease the cost of scientific research.

  16. Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments.

    PubMed

    Armean, Irina M; Lilley, Kathryn S; Trotter, Matthew W B

    2013-01-01

    Advances in sensitivity, resolution, mass accuracy, and throughput have considerably increased the number of protein identifications made via mass spectrometry. Despite these advances, state-of-the-art experimental methods for the study of protein-protein interactions yield more candidate interactions than may be expected biologically owing to biases and limitations in the experimental methodology. In silico methods, which distinguish between true and false interactions, have been developed and applied successfully to reduce the number of false positive results yielded by physical interaction assays. Such methods may be grouped according to: (1) the type of data used: methods based on experiment-specific measurements (e.g., spectral counts or identification scores) versus methods that extract knowledge encoded in external annotations (e.g., public interaction and functional categorisation databases); (2) the type of algorithm applied: the statistical description and estimation of physical protein properties versus predictive supervised machine learning or text-mining algorithms; (3) the type of protein relation evaluated: direct (binary) interaction of two proteins in a cocomplex versus probability of any functional relationship between two proteins (e.g., co-occurrence in a pathway, sub cellular compartment); and (4) initial motivation: elucidation of experimental data by evaluation versus prediction of novel protein-protein interaction, to be experimentally validated a posteriori. This work reviews several popular computational scoring methods and software platforms for protein-protein interactions evaluation according to their methodology, comparative strengths and weaknesses, data representation, accessibility, and availability. The scoring methods and platforms described include: CompPASS, SAINT, Decontaminator, MINT, IntAct, STRING, and FunCoup. References to related work are provided throughout in order to provide a concise but thorough introduction to a

  17. Multi-atlas segmentation with particle-based group-wise image registration.

    PubMed

    Lee, Joohwi; Lyu, Ilwoo; Styner, Martin

    2014-03-21

    We propose a novel multi-atlas segmentation method that employs a group-wise image registration method for the brain segmentation on rodent magnetic resonance (MR) images. The core element of the proposed segmentation is the use of a particle-guided image registration method that extends the concept of particle correspondence into the volumetric image domain. The registration method performs a group-wise image registration that simultaneously registers a set of images toward the space defined by the average of particles. The particle-guided image registration method is robust with low signal-to-noise ratio images as well as differing sizes and shapes observed in the developing rodent brain. Also, the use of an implicit common reference frame can prevent potential bias induced by the use of a single template in the segmentation process. We show that the use of a particle guided-image registration method can be naturally extended to a novel multi-atlas segmentation method and improves the registration method to explicitly use the provided template labels as an additional constraint. In the experiment, we show that our segmentation algorithm provides more accuracy with multi-atlas label fusion and stability against pair-wise image registration. The comparison with previous group-wise registration method is provided as well.

  18. 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

  19. 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.

  20. 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.

  1. Validation of histology image registration

    NASA Astrophysics Data System (ADS)

    Shojaii, Rushin; Karavardanyan, Tigran; Yaffe, Martin; Martel, Anne L.

    2011-03-01

    The aim of this paper is to validate an image registration pipeline used for histology image alignment. In this work a set of histology images are registered to their correspondent optical blockface images to make a histology volume. Then multi-modality fiducial markers are used to validate the alignment of histology images. The fiducial markers are catheters perfused with a mixture of cuttlefish ink and flour. Based on our previous investigations this fiducial marker is visible in medical images, optical blockface images and it can also be localized in histology images. The properties of this fiducial marker make it suitable for validation of the registration techniques used for histology image alignment. This paper reports on the accuracy of a histology image registration approach by calculation of target registration error using these fiducial markers.

  2. Profile-QSAR: a novel meta-QSAR method that combines activities across the kinase family to accurately predict affinity, selectivity, and cellular activity.

    PubMed

    Martin, Eric; Mukherjee, Prasenjit; Sullivan, David; Jansen, Johanna

    2011-08-22

    Profile-QSAR is a novel 2D predictive model building method for kinases. This "meta-QSAR" method models the activity of each compound against a new kinase target as a linear combination of its predicted activities against a large panel of 92 previously studied kinases comprised from 115 assays. Profile-QSAR starts with a sparse incomplete kinase by compound (KxC) activity matrix, used to generate Bayesian QSAR models for the 92 "basis-set" kinases. These Bayesian QSARs generate a complete "synthetic" KxC activity matrix of predictions. These synthetic activities are used as "chemical descriptors" to train partial-least squares (PLS) models, from modest amounts of medium-throughput screening data, for predicting activity against new kinases. The Profile-QSAR predictions for the 92 kinases (115 assays) gave a median external R²(ext) = 0.59 on 25% held-out test sets. The method has proven accurate enough to predict pairwise kinase selectivities with a median correlation of R²(ext) = 0.61 for 958 kinase pairs with at least 600 common compounds. It has been further expanded by adding a "C(k)XC" cellular activity matrix to the KxC matrix to predict cellular activity for 42 kinase driven cellular assays with median R²(ext) = 0.58 for 24 target modulation assays and R²(ext) = 0.41 for 18 cell proliferation assays. The 2D Profile-QSAR, along with the 3D Surrogate AutoShim, are the foundations of an internally developed iterative medium-throughput screening (IMTS) methodology for virtual screening (VS) of compound archives as an alternative to experimental high-throughput screening (HTS). The method has been applied to 20 actual prospective kinase projects. Biological results have so far been obtained in eight of them. Q² values ranged from 0.3 to 0.7. Hit-rates at 10 uM for experimentally tested compounds varied from 25% to 80%, except in K5, which was a special case aimed specifically at finding "type II" binders, where none of the compounds were predicted to be

  3. 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

  4. Detection of protein-protein interactions using tandem affinity purification.

    PubMed

    Goodfellow, Ian; Bailey, Dalan

    2014-01-01

    Tandem affinity purification (TAP) is an invaluable technique for identifying interaction partners for an affinity tagged bait protein. The approach relies on the fusion of dual tags to the bait before separate rounds of affinity purification and precipitation. Frequently two specific elution steps are also performed to increase the specificity of the overall technique. In the method detailed here, the two tags used are protein G and a short streptavidin binding peptide; however, many variations can be employed. In our example the tags are separated by a cleavable tobacco etch virus protease target sequence, allowing for specific elution after the first round of affinity purification. Proteins isolated after the final elution step in this process are concentrated before being identified by mass spectrometry. The use of dual affinity tags and specific elution in this technique dramatically increases both the specificity and stringency of the pull-downs, ensuring a low level of background nonspecific interactions.

  5. 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.

  6. 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

  7. 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

  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. 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.

  10. 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.

  11. 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

    2016-04-20

    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.

  12. 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

  13. 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

  14. 3D ultrasound to stereoscopic camera registration through an air-tissue boundary.

    PubMed

    Yip, Michael C; Adebar, Troy K; Rohling, Robert N; Salcudean, Septimiu E; Nguan, Christopher Y

    2010-01-01

    A novel registration method between 3D ultrasound and stereoscopic cameras is proposed based on tracking a registration tool featuring both ultrasound fiducials and optical markers. The registration tool is pressed against an air-tissue boundary where it can be seen both in ultrasound and in the camera view. By localizing the fiducials in the ultrasound volume, knowing the registration tool geometry, and tracking the tool with the cameras, a registration is found. This method eliminates the need for external tracking, requires minimal setup, and may be suitable for a range of minimally invasive surgeries. A study of the appearance of ultrasound fiducials on an air-tissue boundary is presented, and an initial assessment of the ability to localize the fiducials in ultrasound with sub-millimeter accuracy is provided. The overall accuracy of registration (1.69 +/- 0.60 mm) is a noticeable improvement over other reported methods and warrants patient studies.

  15. Research on registration algorithm for check seal verification

    NASA Astrophysics Data System (ADS)

    Wang, Shuang; Liu, Tiegen

    2008-03-01

    Nowadays seals play an important role in China. With the development of social economy, the traditional method of manual check seal identification can't meet the need s of banking transactions badly. This paper focus on pre-processing and registration algorithm for check seal verification using theory of image processing and pattern recognition. First of all, analyze the complex characteristics of check seals. To eliminate the difference of producing conditions and the disturbance caused by background and writing in check image, many methods are used in the pre-processing of check seal verification, such as color components transformation, linearity transform to gray-scale image, medium value filter, Otsu, close calculations and labeling algorithm of mathematical morphology. After the processes above, the good binary seal image can be obtained. On the basis of traditional registration algorithm, a double-level registration method including rough and precise registration method is proposed. The deflection angle of precise registration method can be precise to 0.1°. This paper introduces the concepts of difference inside and difference outside and use the percent of difference inside and difference outside to judge whether the seal is real or fake. The experimental results of a mass of check seals are satisfied. It shows that the methods and algorithmic presented have good robustness to noise sealing conditions and satisfactory tolerance of difference within class.

  16. Non-rigid image registration with SalphaS filters.

    PubMed

    Liao, Shu; Chung, Albert C S

    2008-01-01

    In this paper, based on the SalphaS distributions, we design SalphaS filters and use the filters as a new feature extraction method for non-rigid medical image registration. In brain MR images, the energy distributions of different frequency bands often exhibit heavy-tailed behavior. Such non-Gaussian behavior is essential for non-rigid image registration but cannot be satisfactorily modeled by the conventional Gabor filters. This leads to unsatisfactory modeling of voxels located at the salient regions of the images. To this end, we propose the SalphaS filters for modeling the heavy-tailed behavior of the energy distributions of brain MR images, and show that the Gabor filter is a special case of the SalphaS filter. The maximum response orientation selection criterion is defined for each frequency band to achieve rotation invariance. In our framework, if the brain MR images are already segmented, each voxel can be automatically assigned a weighting factor based on the Fisher's separation criterion and it is shown that the registration performance can be further improved. The proposed method has been compared with the free-form-deformation based method, Demons algorithm and a method using Gabor features by conducting non-rigid image registration experiments. It is observed that the proposed method achieves the best registration accuracy among all the compared methods in both the simulated and real datasets obtained from the BrainWeb and IBSR respectively.

  17. 21 CFR 1301.35 - Certificate of registration; denial of registration.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... registration. (a) The Administrator shall issue a Certificate of Registration (DEA Form 223) to an applicant if... Federal Register. (c) The Certificate of Registration (DEA Form 223) shall contain the name, address,...

  18. 21 CFR 1309.42 - Certificate of registration; denial of registration.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ...; denial of registration. (a) The Administrator shall issue a Certificate of Registration (DEA Form 511) to..., shall hold a hearing on the application pursuant to § 1309.51. (b) The Certificate of Registration...

  19. 21 CFR 1309.42 - Certificate of registration; denial of registration.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...; denial of registration. (a) The Administrator shall issue a Certificate of Registration (DEA Form 511) to..., shall hold a hearing on the application pursuant to § 1309.51. (b) The Certificate of Registration...

  20. 21 CFR 1301.35 - Certificate of registration; denial of registration.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... registration. (a) The Administrator shall issue a Certificate of Registration (DEA Form 223) to an applicant if... Federal Register. (c) The Certificate of Registration (DEA Form 223) shall contain the name, address,...

  1. 21 CFR 1301.35 - Certificate of registration; denial of registration.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... registration. (a) The Administrator shall issue a Certificate of Registration (DEA Form 223) to an applicant if... Federal Register. (c) The Certificate of Registration (DEA Form 223) shall contain the name, address,...

  2. 21 CFR 1309.42 - Certificate of registration; denial of registration.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ...; denial of registration. (a) The Administrator shall issue a Certificate of Registration (DEA Form 511) to..., shall hold a hearing on the application pursuant to § 1309.51. (b) The Certificate of Registration...

  3. 21 CFR 1301.35 - Certificate of registration; denial of registration.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... registration. (a) The Administrator shall issue a Certificate of Registration (DEA Form 223) to an applicant if... Federal Register. (c) The Certificate of Registration (DEA Form 223) shall contain the name, address,...

  4. 21 CFR 1301.35 - Certificate of registration; denial of registration.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... registration. (a) The Administrator shall issue a Certificate of Registration (DEA Form 223) to an applicant if... Federal Register. (c) The Certificate of Registration (DEA Form 223) shall contain the name, address,...

  5. 21 CFR 1309.42 - Certificate of registration; denial of registration.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...; denial of registration. (a) The Administrator shall issue a Certificate of Registration (DEA Form 511) to..., shall hold a hearing on the application pursuant to § 1309.51. (b) The Certificate of Registration...

  6. Automated landmark-guided deformable image registration

    NASA Astrophysics Data System (ADS)

    Kearney, Vasant; Chen, Susie; Gu, Xuejun; Chiu, Tsuicheng; Liu, Honghuan; Jiang, Lan; Wang, Jing; Yordy, John; Nedzi, Lucien; Mao, Weihua

    2015-01-01

    The purpose of this work is to develop an automated landmark-guided deformable image registration (LDIR) algorithm between the planning CT and daily cone-beam CT (CBCT) with low image quality. This method uses an automated landmark generation algorithm in conjunction with a local small volume gradient matching search engine to map corresponding landmarks between the CBCT and the planning CT. The landmarks act as stabilizing control points in the following Demons deformable image registration. LDIR is implemented on graphics processing units (GPUs) for parallel computation to achieve ultra fast calculation. The accuracy of the LDIR algorithm has been evaluated on a synthetic case in the presence of different noise levels and data of six head and neck cancer patients. The results indicate that LDIR performed better than rigid registration, Demons, and intensity corrected Demons for all similarity metrics used. In conclusion, LDIR achieves high accuracy in the presence of multimodality intensity mismatch and CBCT noise contamination, while simultaneously preserving high computational efficiency.

  7. Automated landmark-guided deformable image registration.

    PubMed

    Kearney, Vasant; Chen, Susie; Gu, Xuejun; Chiu, Tsuicheng; Liu, Honghuan; Jiang, Lan; Wang, Jing; Yordy, John; Nedzi, Lucien; Mao, Weihua

    2015-01-01

    The purpose of this work is to develop an automated landmark-guided deformable image registration (LDIR) algorithm between the planning CT and daily cone-beam CT (CBCT) with low image quality. This method uses an automated landmark generation algorithm in conjunction with a local small volume gradient matching search engine to map corresponding landmarks between the CBCT and the planning CT. The landmarks act as stabilizing control points in the following Demons deformable image registration. LDIR is implemented on graphics processing units (GPUs) for parallel computation to achieve ultra fast calculation. The accuracy of the LDIR algorithm has been evaluated on a synthetic case in the presence of different noise levels and data of six head and neck cancer patients. The results indicate that LDIR performed better than rigid registration, Demons, and intensity corrected Demons for all similarity metrics used. In conclusion, LDIR achieves high accuracy in the presence of multimodality intensity mismatch and CBCT noise contamination, while simultaneously preserving high computational efficiency. PMID:25479095

  8. Mammogram CAD, hybrid registration and iconic analysis

    NASA Astrophysics Data System (ADS)

    Boucher, A.; Cloppet, F.; Vincent, N.

    2013-03-01

    This paper aims to develop a computer aided diagnosis (CAD) based on a two-step methodology to register and analyze pairs of temporal mammograms. The concept of "medical file", including all the previous medical information on a patient, enables joint analysis of different acquisitions taken at different times, and the detection of significant modifications. The developed registration method aims to superimpose at best the different anatomical structures of the breast. The registration is designed in order to get rid of deformation undergone by the acquisition process while preserving those due to breast changes indicative of malignancy. In order to reach this goal, a referent image is computed from control points based on anatomical features that are extracted automatically. Then the second image of the couple is realigned on the referent image, using a coarse-to-fine approach according to expert knowledge that allows both rigid and non-rigid transforms. The joint analysis detects the evolution between two images representing the same scene. In order to achieve this, it is important to know the registration error limits in order to adapt the observation scale. The approach used in this paper is based on an image sparse representation. Decomposed in regular patterns, the images are analyzed under a new angle. The evolution detection problem has many practical applications, especially in medical images. The CAD is evaluated using recall and precision of differences in mammograms.

  9. The Quality of Registration of Clinical Trials

    PubMed Central

    Viergever, Roderik F.; Ghersi, Davina

    2011-01-01

    Background Lack of transparency in clinical trial conduct, publication bias and selective reporting bias are still important problems in medical research. Through clinical trials registration, it should be possible to take steps towards resolving some of these problems. However, previous evaluations of registered records of clinical trials have shown that registered information is often incomplete and non-meaningful. If these studies are accurate, this negates the possible benefits of registration of clinical trials. Methods and Findings A 5% sample of records of clinical trials that were registered between 17 June 2008 and 17 June 2009 was taken from the International Clinical Trials Registry Platform (ICTRP) database and assessed for the presence of contact information, the presence of intervention specifics in drug trials and the quality of primary and secondary outcome reporting. 731 records were included. More than half of the records were registered after recruitment of the first participant. The name of a contact person was available in 94.4% of records from non-industry funded trials and 53.7% of records from industry funded trials. Either an email address or a phone number was present in 76.5% of non-industry funded trial records and in 56.5% of industry funded trial records. Although a drug name or company serial number was almost always provided, other drug intervention specifics were often omitted from registration. Of 3643 reported outcomes, 34.9% were specific measures with a meaningful time frame. Conclusions Clinical trials registration has the potential to contribute substantially to improving clinical trial transparency and reducing publication bias and selective reporting. These potential benefits are currently undermined by deficiencies in the provision of information in key areas of registered records. PMID:21383991

  10. Implicit reference-based group-wise image registration and its application to structural and functional MRI.

    PubMed

    Geng, Xiujuan; Christensen, Gary E; Gu, Hong; Ross, Thomas J; Yang, Yihong

    2009-10-01

    In this study, an implicit reference group-wise (IRG) registration with a small deformation, linear elastic model was used to jointly estimate correspondences between a set of MRI images. The performance of pair-wise and group-wise registration algorithms was evaluated for spatial normalization of structural and functional MRI data. Traditional spatial normalization is accomplished by group-to-reference (G2R) registration in which a group of images are registered pair-wise to a reference image. G2R registration is limited due to bias associated with selecting a reference image. In contrast, implicit reference group-wise (IRG) registration estimates correspondences between a group of images by jointly registering the images to an implicit reference corresponding to the group average. The implicit reference is estimated during IRG registration eliminating the bias associated with selecting a specific reference image. Registration performance was evaluated using segmented T1-weighted magnetic resonance images from the Nonrigid Image Registration Evaluation Project (NIREP), DTI and fMRI images. Implicit reference pair-wise (IRP) registration-a special case of IRG registration for two images-is shown to produce better relative overlap than IRG for pair-wise registration using the same small deformation, linear elastic registration model. However, IRP-G2R registration is shown to have significant transitivity error, i.e., significant inconsistencies between correspondences defined by different pair-wise transformations. In contrast, IRG registration produces consistent correspondence between images in a group at the cost of slightly reduced pair-wise RO accuracy compared to IRP-G2R. IRG spatial normalization of the fractional anisotropy (FA) maps of DTI is shown to have smaller FA variance compared with G2R methods using the same elastic registration model. Analyses of fMRI data sets with sensorimotor and visual tasks show that IRG registration, on average, increases the

  11. Pydpiper: a flexible toolkit for constructing novel registration pipelines

    PubMed Central

    Friedel, Miriam; van Eede, Matthijs C.; Pipitone, Jon; Chakravarty, M. Mallar; Lerch, Jason P.

    2014-01-01

    Using neuroimaging technologies to elucidate the relationship between genotype and phenotype and brain and behavior will be a key contribution to biomedical research in the twenty-first century. Among the many methods for analyzing neuroimaging data, image registration deserves particular attention due to its wide range of applications. Finding strategies to register together many images and analyze the differences between them can be a challenge, particularly given that different experimental designs require different registration strategies. Moreover, writing software that can handle different types of image registration pipelines in a flexible, reusable and extensible way can be challenging. In response to this challenge, we have created Pydpiper, a neuroimaging registration toolkit written in Python. Pydpiper is an open-source, freely available software package that provides multiple modules for various image registration applications. Pydpiper offers five key innovations. Specifically: (1) a robust file handling class that allows access to outputs from all stages of registration at any point in the pipeline; (2) the ability of the framework to eliminate duplicate stages; (3) reusable, easy to subclass modules; (4) a development toolkit written for non-developers; (5) four complete applications that run complex image registration pipelines “out-of-the-box.” In this paper, we will discuss both the general Pydpiper framework and the various ways in which component modules can be pieced together to easily create new registration pipelines. This will include a discussion of the core principles motivating code development and a comparison of Pydpiper with other available toolkits. We also provide a comprehensive, line-by-line example to orient users with limited programming knowledge and highlight some of the most useful features of Pydpiper. In addition, we will present the four current applications of the code. PMID:25126069

  12. Early Birth Registration at a Center in Rural India

    PubMed Central

    Sachdeva, Sandeep; Nagar, Mukesh; Tyagi, Ajay; Sachdeva, Ruchi; Kumar, Vijay

    2013-01-01

    Background: Registration of birth is mandatory in India however due to various issues compliance for timely birth registration has been poor. Objective: The objective of this study was to determine time elapsed between birth and registration and describe the socio-demographic profile of registered births at a rural center. Materials and Methods: A cross-sectional descriptive study was undertaken and all births registered at a primary health center of a block during the period 2010 and 2011 were retrieved and data collection carried using structured proforma based on birth formats under civil registration system (CRS). House to house visit was undertaken to identify births without registration. Results: A total of 340 and 276 births were registered during 2010 and 2011 respectively. Time elapsed between birth and registration was computed to be lower, i.e., 9.38 days (±7.46) during 2011 in-comparison with 10.52 days (±8.73) in 2010. On a positive note, higher level of education and marriage of women beyond legal age of 18 years was noticed in 2011 in comparison with 2010. Overall, institutional birth stood at a very encouraging note (66.2%). All (100%) births during the study period were registered at this (rural) or higher center (urban) depending on the place of delivery. An omission/commission of birth format is highlighted that needs urgent attention of the authorities. Discussion: Majority (>92%) of birth registration occurred with-in the stipulated period of 21 days as prescribed under CRS and our study indicates early birth registration in a rural area of Haryana, India. PMID:24479089

  13. 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

  14. Registration and 3D visualization of large microscopy images

    NASA Astrophysics Data System (ADS)

    Mosaliganti, Kishore; Pan, Tony; Sharp, Richard; Ridgway, Randall; Iyengar, Srivathsan; Gulacy, Alexandra; Wenzel, Pamela; de Bruin, Alain; Machiraju, Raghu; Huang, Kun; Leone, Gustavo; Saltz, Joel

    2006-03-01

    Inactivation of the retinoblastoma gene in mouse embryos causes tissue infiltrations into critical sections of the placenta, which has been shown to affect fetal survivability. Our collaborators in cancer genetics are extremely interested in examining the three dimensional nature of these infiltrations given a stack of two dimensional light microscopy images. Three sets of wildtype and mutant placentas was sectioned serially and digitized using a commercial light microscopy scanner. Each individual placenta dataset consisted of approximately 1000 images totaling 700 GB in size, which were registered into a volumetric dataset using National Library of Medicine's (NIH/NLM) Insight Segmentation and Registration Toolkit (ITK). This paper describes our method for image registration to aid in volume visualization of tissue level intermixing for both wildtype and Rb - specimens. The registration process faces many challenges arising from the large image sizes, damages during sectioning, staining gradients both within and across sections, and background noise. These issues limit the direct application of standard registration techniques due to frequent convergence to local solutions. In this work, we develop a mixture of automated and semi-automated enhancements with ground-truth validation for the mutual information-based registration algorithm. Our final volume renderings clearly show tissue intermixing differences between both wildtype and Rb - specimens which are not obvious prior to registration.

  15. Accuracy assessment of fluoroscopy-transesophageal echocardiography registration

    NASA Astrophysics Data System (ADS)

    Lang, Pencilla; Seslija, Petar; Bainbridge, Daniel; Guiraudon, Gerard M.; Jones, Doug L.; Chu, Michael W.; Holdsworth, David W.; Peters, Terry M.

    2011-03-01

    This study assesses the accuracy of a new transesophageal (TEE) ultrasound (US) fluoroscopy registration technique designed to guide percutaneous aortic valve replacement. In this minimally invasive procedure, a valve is inserted into the aortic annulus via a catheter. Navigation and positioning of the valve is guided primarily by intra-operative fluoroscopy. Poor anatomical visualization of the aortic root region can result in incorrect positioning, leading to heart valve embolization, obstruction of the coronary ostia and acute kidney injury. The use of TEE US images to augment intra-operative fluoroscopy provides significant improvements to image-guidance. Registration is achieved using an image-based TEE probe tracking technique and US calibration. TEE probe tracking is accomplished using a single-perspective pose estimation algorithm. Pose estimation from a single image allows registration to be achieved using only images collected in standard OR workflow. Accuracy of this registration technique is assessed using three models: a point target phantom, a cadaveric porcine heart with implanted fiducials, and in-vivo porcine images. Results demonstrate that registration can be achieved with an RMS error of less than 1.5mm, which is within the clinical accuracy requirements of 5mm. US-fluoroscopy registration based on single-perspective pose estimation demonstrates promise as a method for providing guidance to percutaneous aortic valve replacement procedures. Future work will focus on real-time implementation and a visualization system that can be used in the operating room.

  16. 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

  17. Mask registration and wafer overlay

    NASA Astrophysics Data System (ADS)

    Lee, Chulseung; Bang, Changjin; Kim, Myoungsoo; Kang, Hyosang; Lee, Dohwa; Jeong, Woonjae; Lim, Ok-Sung; Yoon, Seunghoon; Jung, Jaekang; Laske, Frank; Parisoli, Lidia; Roeth, Klaus-Dieter; Robinson, John C.; Jug, Sven; Izikson, Pavel; Dinu, Berta; Widmann, Amir; Choi, DongSub

    2010-03-01

    Overlay continues to be one of the key challenges for lithography in advanced semiconductor manufacturing. It becomes even more challenging due to the continued shrinking of the device node. Some low k1 techniques, such as Double Exposure and Double Patterning also add additional loss of the overlay margin due to the fact that the single layer pattern is created based on more than 1 exposure. Therefore, the overlay between 2 exposures requires very tight overlay specification. Mask registration is one of the major contributors to wafer overlay, especially field related overlay. We investigated mask registration and wafer overlay by co-analyzing the mask data and the wafer overlay data. To achieve the accurate cohesive results, we introduced the combined metrology mark which can be used for both mask registration measurement as well as for wafer overlay measurement. Coincidence of both metrology marks make it possible to subtract mask signature from wafer overlay without compromising the accuracy due to the physical distance between measurement marks, if we use 2 different marks for both metrologies. Therefore, it is possible to extract pure scanner related signatures, and to analyze the scanner related signatures in details to in order to enable root cause analysis and ultimately drive higher wafer yield. We determined the exact mask registration error in order to decompose wafer overlay into mask, scanner, process and metrology. We also studied the impact of pellicle mounting by comparison of mask registration measurement pre-pellicle mounting and post-pellicle mounting in this investigation.

  18. Iterative edge- and wavelet-based image registration of AVHRR and GOES satellite imagery

    NASA Technical Reports Server (NTRS)

    LeMoigne, Jacqueline; El-Saleous, Nazmi; Vermote, Eric

    1997-01-01

    Most automatic registration methods are either correlation-based, feature-based, or a combination of both. Examples of features which can be utilized for automatic image registration are edges, regions, corners, or wavelet-extracted features. In this paper, we describe two proposed approaches, based on edge or edge-like features, which are very appropriate to highlight regions of interest such as coastlines. The two iterative methods utilize the Normalized Cross-Correlation of edge and wavelet features and are applied to such problems as image-to-map registration, landmarking, and channel-to-channel co-registration, utilizing test data, AVHRR data, as well as GOES image data.

  19. Simultaneous registration and segmentation of images in wavelet domain

    NASA Astrophysics Data System (ADS)

    Yoshida, Hiroyuki

    1999-10-01

    A novel method for simultaneous registration and segmentation is developed. The method is designed to register two similar images while a region with significant difference is adaptively segmented. This is achieved by minimization of a non-linear functional that models the statistical properties of the subtraction of the two images. Minimization is performed in the wavelet domain by a coarse- to-fine approach to yield a mapping that yields the registration and the boundary that yields the segmentation. The new method was applied to the registration of the left and the right lung regions in chest radiographs for extraction of lung nodules while the normal anatomic structures such as ribs are removed. A preliminary result shows that our method is very effective in reducing the number of false detections obtained with our computer-aided diagnosis scheme for detection of lung nodules in chest radiographs.

  20. Invariant Feature Matching for Image Registration Application Based on New Dissimilarity of Spatial Features.

    PubMed

    Mousavi Kahaki, Seyed Mostafa; Nordin, Md Jan; Ashtari, Amir H; J Zahra, Sophia

    2016-01-01

    An invariant feature matching method is proposed as a spatially invariant feature matching approach. Deformation effects, such as affine and homography, change the local information within the image and can result in ambiguous local information pertaining to image points. New method based on dissimilarity values, which measures the dissimilarity of the features through the path based on Eigenvector properties, is proposed. Evidence shows that existing matching techniques using similarity metrics--such as normalized cross-correlation, squared sum of intensity differences and correlation coefficient--are insufficient for achieving adequate results under different image deformations. Thus, new descriptor's similarity metrics based on normalized Eigenvector correlation and signal directional differences, which are robust under local variation of the image information, are proposed to establish an efficient feature matching technique. The method proposed in this study measures the dissimilarity in the signal frequency along the path between two features. Moreover, these dissimilarity values are accumulated in a 2D dissimilarity space, allowing accurate corresponding features to be extracted based on the cumulative space using a voting strategy. This method can be used in image registration applications, as it overcomes the limitations of the existing approaches. The output results demonstrate that the proposed technique outperforms the other methods when evaluated using a standard dataset, in terms of precision-recall and corner correspondence. PMID:26985996

  1. Invariant Feature Matching for Image Registration Application Based on New Dissimilarity of Spatial Features

    PubMed Central

    Mousavi Kahaki, Seyed Mostafa; Nordin, Md Jan; Ashtari, Amir H.; J. Zahra, Sophia

    2016-01-01

    An invariant feature matching method is proposed as a spatially invariant feature matching approach. Deformation effects, such as affine and homography, change the local information within the image and can result in ambiguous local information pertaining to image points. New method based on dissimilarity values, which measures the dissimilarity of the features through the path based on Eigenvector properties, is proposed. Evidence shows that existing matching techniques using similarity metrics—such as normalized cross-correlation, squared sum of intensity differences and correlation coefficient—are insufficient for achieving adequate results under different image deformations. Thus, new descriptor’s similarity metrics based on normalized Eigenvector correlation and signal directional differences, which are robust under local variation of the image information, are proposed to establish an efficient feature matching technique. The method proposed in this study measures the dissimilarity in the signal frequency along the path between two features. Moreover, these dissimilarity values are accumulated in a 2D dissimilarity space, allowing accurate corresponding features to be extracted based on the cumulative space using a voting strategy. This method can be used in image registration applications, as it overcomes the limitations of the existing approaches. The output results demonstrate that the proposed technique outperforms the other methods when evaluated using a standard dataset, in terms of precision-recall and corner correspondence. PMID:26985996

  2. "Clickable" agarose for affinity chromatography.

    PubMed

    Punna, Sreenivas; Kaltgrad, Eiton; Finn, M G

    2005-01-01

    Successful purification of biological molecules by affinity chromatography requires the attachment of desired ligands to biocompatible chromatographic supports. The Cu(I)-catalyzed cycloaddition of azides and alkynes-the premier example of "click chemistry"-is an efficient way to make covalent connections among diverse molecules and materials. Both azide and alkyne units are highly selective in their reactivity, being inert to most chemical functionalities and stable to wide ranges of solvent, temperature, and pH. We show that agarose beads bearing alkyne and azide groups can be easily made and are practical precursors to functionalized agarose materials for affinity chromatography.

  3. 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

  4. 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.

  5. Can dental registrants use the Index of Orthodontic Treatment Need accurately? Part 1: Knowledge of IOTN among dental registrants.

    PubMed

    Jawad, Z; Bates, C; Hodge, T

    2016-05-27

    Aim To determine whether dental registrants can use the dental health component (DHC) and aesthetic component (AC) of the Index of Orthodontic Treatment Need (IOTN) 'accurately' to an acceptable level of agreement and diagnostic validity.Method Participants from six different registrant groups were asked to score the IOTN for 14 cases based on study models and photographs as well as completing a short questionnaire. Participants in the study were all recruited at study days and annual conferences. The main outcome measures include the different registrant groups IOTN scores compared to expert panel scores using kappa statistics. To assess for diagnostic validity, individual participants sensitivity and specificity scores were calculated.Result Overall, 229 registrants took part in the study. For the DHC the specialist orthodontist (SO), postgraduate orthodontic student (PGOS) and the qualified orthodontic therapist (QOT) groups achieved a mean kappa ≥0.60 indicating 'acceptable' agreement with the expert panel scores. The dental foundation trainee (DFT) and general dental practitioner (GDP) group achieved a mean kappa of 0.20 and 0.22 respectively indicating poor and fair agreement. The student orthodontic therapist (SOT) group achieved a mean kappa of 0.55 indicating moderate agreement. For the AC none of the registrant groups achieved an acceptable level of agreement with the mean kappa scores for the different groups ranging from kappa 0.13-0.21, indicating poor to fair agreement.Conclusion Overall agreement for the DHC was varied for the different registrant groups ranging from fair to substantial agreement. Registrants were better at applying the DHC compared to the AC with agreement ranging from poor to fair. More needs to done to help registrants use the IOTN more 'accurately'.

  6. Feasibility of Multimodal Deformable Registration for Head and Neck Tumor Treatment Planning

    SciTech Connect

    Fortunati, Valerio; Verhaart, René F.; Angeloni, Francesco; Lugt, Aad van der; Niessen, Wiro J.; Veenland, Jifke F.; Paulides, Margarethus M.; Walsum, Theo van

    2014-09-01

    Purpose: To investigate the feasibility of using deformable registration in clinical practice to fuse MR and CT images of the head and neck for treatment planning. Method and Materials: A state-of-the-art deformable registration algorithm was optimized, evaluated, and compared with rigid registration. The evaluation was based on manually annotated anatomic landmarks and regions of interest in both modalities. We also developed a multiparametric registration approach, which simultaneously aligns T1- and T2-weighted MR sequences to CT. This was evaluated and compared with single-parametric approaches. Results: Our results show that deformable registration yielded a better accuracy than rigid registration, without introducing unrealistic deformations. For deformable registration, an average landmark alignment of approximatively 1.7 mm was obtained. For all the regions of interest excluding the cerebellum and the parotids, deformable registration provided a median modified Hausdorff distance of approximatively 1 mm. Similar accuracies were obtained for the single-parameter and multiparameter approaches. Conclusions: This study demonstrates that deformable registration of head-and-neck CT and MR images is feasible, with overall a significanlty higher accuracy than for rigid registration.

  7. Language proficiency and nursing registration.

    PubMed

    Müller, Amanda

    2016-02-01

    This discussion paper focuses on English proficiency standards for nursing registration in Australia, how Australia has dealt with the issue of language proficiency, and the factors which have led to the establishment of the current language standards. Also, this paper will provide a comparison of the two language tests that are currently accepted in Australia (OET and IELTS), including the appropriateness of these tests and the minimum standards used. The paper will also examine the use of educational background as an indicator of language proficiency. Finally, communication-based complaints in the post-registration environment will be explored, and some discussion will be provided about why pre-registration measures might have failed to prevent such problematic situations from occurring.

  8. Language proficiency and nursing registration.

    PubMed

    Müller, Amanda

    2016-02-01

    This discussion paper focuses on English proficiency standards for nursing registration in Australia, how Australia has dealt with the issue of language proficiency, and the factors which have led to the establishment of the current language standards. Also, this paper will provide a comparison of the two language tests that are currently accepted in Australia (OET and IELTS), including the appropriateness of these tests and the minimum standards used. The paper will also examine the use of educational background as an indicator of language proficiency. Finally, communication-based complaints in the post-registration environment will be explored, and some discussion will be provided about why pre-registration measures might have failed to prevent such problematic situations from occurring. PMID:25704372

  9. Registration of interferometric SAR images

    NASA Technical Reports Server (NTRS)

    Lin, Qian; Vesecky, John F.; Zebker, Howard A.

    1992-01-01

    Interferometric synthetic aperture radar (INSAR) is a new way of performing topography mapping. Among the factors critical to mapping accuracy is the registration of the complex SAR images from repeated orbits. A new algorithm for registering interferometric SAR images is presented. A new figure of merit, the average fluctuation function of the phase difference image, is proposed to evaluate the fringe pattern quality. The process of adjusting the registration parameters according to the fringe pattern quality is optimized through a downhill simplex minimization algorithm. The results of applying the proposed algorithm to register two pairs of Seasat SAR images with a short baseline (75 m) and a long baseline (500 m) are shown. It is found that the average fluctuation function is a very stable measure of fringe pattern quality allowing very accurate registration.

  10. Hierarchical and symmetric infant image registration by robust longitudinal-example-guided correspondence detection

    PubMed Central

    Wu, Yao; Wu, Guorong; Wang, Li; Munsell, Brent C.; Wang, Qian; Lin, Weili; Feng, Qianjin; Chen, Wufan; Shen, Dinggang

    2015-01-01

    Purpose: To investigate anatomical differences across individual subjects, or longitudinal changes in early brain development, it is important to perform accurate image registration. However, due to fast brain development and dynamic tissue appearance changes, it is very difficult to align infant brain images acquired from birth to 1-yr-old. Methods: To solve this challenging problem, a novel image registration method is proposed to align two infant brain images, regardless of age at acquisition. The main idea is to utilize the growth trajectories, or spatial-temporal correspondences, learned from a set of longitudinal training images, for guiding the registration of two different time-point images with different image appearances. Specifically, in the training stage, an intrinsic growth trajectory is first estimated for each training subject using the longitudinal images. To register two new infant images with potentially a large age gap, the corresponding images patches between each new image and its respective training images with similar age are identified. Finally, the registration between the two new images can be assisted by the learned growth trajectories from one time point to another time point that have been established in the training stage. To further improve registration accuracy, the proposed method is combined with a hierarchical and symmetric registration framework that can iteratively add new key points in both images to steer the estimation of the deformation between the two infant brain images under registration. Results: To evaluate image registration accuracy, the proposed method is used to align 24 infant subjects at five different time points (2-week-old, 3-month-old, 6-month-old, 9-month-old, and 12-month-old). Compared to the state-of-the-art methods, the proposed method demonstrated superior registration performance. Conclusions: The proposed method addresses the difficulties in the infant brain registration and produces better results

  11. Nonrigid Medical Image Registration Based on Mesh Deformation Constraints

    PubMed Central

    Qiu, TianShuang; Guo, DongMei

    2013-01-01

    Regularizing the deformation field is an important aspect in nonrigid medical image registration. By covering the template image with a triangular mesh, this paper proposes a new regularization constraint in terms of connections between mesh vertices. The connection relationship is preserved by the spring analogy method. The method is evaluated by registering cerebral magnetic resonance imaging (MRI) image data obtained from different individuals. Experimental results show that the proposed method has good deformation ability and topology-preserving ability, providing a new way to the nonrigid medical image registration. PMID:23424604

  12. SU-E-J-132: Automated Segmentation with Post-Registration Atlas Selection Based On Mutual Information

    SciTech Connect

    Ren, X; Gao, H; Sharp, G

    2015-06-15

    Purpose: The delineation of targets and organs-at-risk is a critical step during image-guided radiation therapy, for which manual contouring is the gold standard. However, it is often time-consuming and may suffer from intra- and inter-rater variability. The purpose of this work is to investigate the automated segmentation. Methods: The automatic segmentation here is based on mutual information (MI), with the atlas from Public Domain Database for Computational Anatomy (PDDCA) with manually drawn contours.Using dice coefficient (DC) as the quantitative measure of segmentation accuracy, we perform leave-one-out cross-validations for all PDDCA images sequentially, during which other images are registered to each chosen image and DC is computed between registered contour and ground truth. Meanwhile, six strategies, including MI, are selected to measure the image similarity, with MI to be the best. Then given a target image to be segmented and an atlas, automatic segmentation consists of: (a) the affine registration step for image positioning; (b) the active demons registration method to register the atlas to the target image; (c) the computation of MI values between the deformed atlas and the target image; (d) the weighted image fusion of three deformed atlas images with highest MI values to form the segmented contour. Results: MI was found to be the best among six studied strategies in the sense that it had the highest positive correlation between similarity measure (e.g., MI values) and DC. For automated segmentation, the weighted image fusion of three deformed atlas images with highest MI values provided the highest DC among four proposed strategies. Conclusion: MI has the highest correlation with DC, and therefore is an appropriate choice for post-registration atlas selection in atlas-based segmentation. Xuhua Ren and Hao Gao were partially supported by the NSFC (#11405105), the 973 Program (#2015CB856000) and the Shanghai Pujiang Talent Program (#14PJ1404500)

  13. Locating seed points for automatic multi-organ segmentation using non-rigid registration and organ annotations

    NASA Astrophysics Data System (ADS)

    Joyseeree, Ranveer R.; Müller, Henning

    2015-03-01

    Organ segmentation is helpful for decision-support in diagnostic medicine. Region-growing segmentation algorithms are popular but usually require that clinicians place seed points in structures manually. A method to automatically calculate the seed points for segmenting organs in three-dimensional (3D), non-annotated Computed Tomography (CT) and Magnetic Resonance (MR) volumes from the VISCERAL dataset is presented in this paper. It precludes the need for manual placement of seeds, thereby saving time. It also has the advantage of being a simple yet effective means of finding reliable seed points for segmentation. Affine registration followed by B-spline registration are used to align expert annotations of each organ of interest in order to build a probability map for their respective location in a chosen reference frame. The centroid of each is determined. The same registration framework as above is used to warp the calculated centroids onto the volumes to be segmented. Existing segmentation algorithms may then be applied with the mapped centroids as seed points and the warped probability maps as an aid to the stopping criteria for segmentation. The above method was tested on contrast{enhanced, thorax-abdomen CT images to see if calculated centroids lay within target organs, which would equate to successful segmentation if an effective segmentation algorithm were used. Promising results were obtained and are presented in this paper. The causes for observed failures were identified and countermeasures were proposed in order to achieve even better results in the next stage of development that will involve a wider variety of MR and CT images.

  14. Automatic registration of serial mammary gland sections

    SciTech Connect

    Arganda-Carreras, Ignacio; Fernandez-Gonzalez, Rodrigo; Ortiz-de-Solorzano, Carlos

    2004-04-13

    We present two new methods for automatic registration of microscope images of consecutive tissue sections. They represent two possibilities for the first step in the 3-D reconstruction of histological structures from serially sectioned tissue blocks. The goal is to accurately align the sections in order to place every relevant shape contained in each image in front of its corresponding shape in the following section before detecting the structures of interest and rendering them in 3D. This is accomplished by finding the best rigid body transformation (translation and rotation) of the image being registered by maximizing a matching function based on the image content correlation. The first method makes use of the entire image information, whereas the second one uses only the information located at specific sites, as determined by the segmentation of the most relevant tissue structures. To reduce computing time, we use a multiresolution pyramidal approach that reaches the best registration transformation in increasing resolution steps. In each step, a subsampled version of the images is used. Both methods rely on a binary image which is a thresholded version of the Sobel gradients of the image (first method) or a set of boundaries manually or automatically obtained that define important histological structures of the sections. Then distance-transform of the binary image is computed. A proximity function is then calculated between the distance image of the image being registered and that of the reference image. The transformation providing a maximum of the proximity function is then used as the starting point of the following step. This is iterated until the registration error lies below a minimum value.

  15. Evaluation of registration accuracy between Sentinel-2 and Landsat 8

    NASA Astrophysics Data System (ADS)

    Barazzetti, Luigi; Cuca, Branka; Previtali, Mattia

    2016-08-01

    Starting from June 2015, Sentinel-2A is delivering high resolution optical images (ground resolution up to 10 meters) to provide a global coverage of the Earth's land surface every 10 days. The planned launch of Sentinel-2B along with the integration of Landsat images will provide time series with an unprecedented revisit time indispensable for numerous monitoring applications, in which high resolution multi-temporal information is required. They include agriculture, water bodies, natural hazards to name a few. However, the combined use of multi-temporal images requires an accurate geometric registration, i.e. pixel-to-pixel correspondence for terrain-corrected products. This paper presents an analysis of spatial co-registration accuracy for several datasets of Sentinel-2 and Landsat 8 images distributed all around the world. Images were compared with digital correlation techniques for image matching, obtaining an evaluation of registration accuracy with an affine transformation as geometrical model. Results demonstrate that sub-pixel accuracy was achieved between 10 m resolution Sentinel-2 bands (band 3) and 15 m resolution panchromatic Landsat images (band 8).

  16. Affine differential geometry analysis of human arm movements.

    PubMed

    Flash, Tamar; Handzel, Amir A

    2007-06-01

    Humans interact with their environment through sensory information and motor actions. These interactions may be understood via the underlying geometry of both perception and action. While the motor space is typically considered by default to be Euclidean, persistent behavioral observations point to a different underlying geometric structure. These observed regularities include the "two-thirds power law", which connects path curvature with velocity, and "local isochrony", which prescribes the relation between movement time and its extent. Starting with these empirical observations, we have developed a mathematical framework based on differential geometry, Lie group theory and Cartan's moving frame method for the analysis of human hand trajectories. We also use this method to identify possible motion primitives, i.e., elementary building blocks from which more complicated movements are constructed. We show that a natural geometric description of continuous repetitive hand trajectories is not Euclidean but equi-affine. Specifically, equi-affine velocity is piecewise constant along movement segments, and movement execution time for a given segment is proportional to its equi-affine arc-length. Using this mathematical framework, we then analyze experimentally recorded drawing movements. To examine movement segmentation and classification, the two fundamental equi-affine differential invariants-equi-affine arc-length and curvature are calculated for the recorded movements. We also discuss the possible role of conic sections, i.e., curves with constant equi-affine curvature, as motor primitives and focus in more detail on parabolas, the equi-affine geodesics. Finally, we explore possible schemes for the internal neural coding of motor commands by showing that the equi-affine framework is compatible with the common model of population coding of the hand velocity vector when combined with a simple assumption on its dynamics. We then discuss several alternative explanations

  17. Demons deformable registration for CBCT-guided procedures in the head and neck: Convergence and accuracy

    SciTech Connect

    Nithiananthan, S.; Brock, K. K.; Daly, M. J.; Chan, H.; Irish, J. C.; Siewerdsen, J. H.

    2009-10-15

    Purpose: The accuracy and convergence behavior of a variant of the Demons deformable registration algorithm were investigated for use in cone-beam CT (CBCT)-guided procedures of the head and neck. Online use of deformable registration for guidance of therapeutic procedures such as image-guided surgery or radiation therapy places trade-offs on accuracy and computational expense. This work describes a convergence criterion for Demons registration developed to balance these demands; the accuracy of a multiscale Demons implementation using this convergence criterion is quantified in CBCT images of the head and neck. Methods: Using an open-source ''symmetric'' Demons registration algorithm, a convergence criterion based on the change in the deformation field between iterations was developed to advance among multiple levels of a multiscale image pyramid in a manner that optimized accuracy and computation time. The convergence criterion was optimized in cadaver studies involving CBCT images acquired using a surgical C-arm prototype modified for 3D intraoperative imaging. CBCT-to-CBCT registration was performed and accuracy was quantified in terms of the normalized cross-correlation (NCC) and target registration error (TRE). The accuracy and robustness of the algorithm were then tested in clinical CBCT images of ten patients undergoing radiation therapy of the head and neck. Results: The cadaver model allowed optimization of the convergence factor and initial measurements of registration accuracy: Demons registration exhibited TRE=(0.8{+-}0.3) mm and NCC=0.99 in the cadaveric head compared to TRE=(2.6{+-}1.0) mm and NCC=0.93 with rigid registration. Similarly for the patient data, Demons registration gave mean TRE=(1.6{+-}0.9) mm compared to rigid registration TRE=(3.6{+-}1.9) mm, suggesting registration accuracy at or near the voxel size of the patient images (1x1x2 mm{sup 3}). The multiscale implementation based on optimal convergence criteria completed registration in

  18. 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

  19. Subspace-Based Holistic Registration for Low-Resolution Facial Images

    NASA Astrophysics Data System (ADS)

    Boom, B. J.; Spreeuwers, L. J.; Veldhuis, R. N. J.

    2010-12-01

    Subspace-based holistic registration is introduced as an alternative to landmark-based face registration, which has a poor performance on low-resolution images, as obtained in camera surveillance applications. The proposed registration method finds the alignment by maximizing the similarity score between a probe and a gallery image. We use a novel probabilistic framework for both user-independent as well as user-specific face registration. The similarity is calculated using the probability that the face image is correctly aligned in a face subspace, but additionally we take the probability into account that the face is misaligned based on the residual error in the dimensions perpendicular to the face subspace. We perform extensive experiments on the FRGCv2 database to evaluate the impact that the face registration methods have on face recognition. Subspace-based holistic registration on low-resolution images can improve face recognition in comparison with landmark-based registration on high-resolution images. The performance of the tested face recognition methods after subspace-based holistic registration on a low-resolution version of the FRGC database is similar to that after manual registration.

  20. 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…

  1. 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.…

  2. How Structure Defines Affinity in Protein-Protein Interactions

    PubMed Central

    Erijman, Ariel; Rosenthal, Eran; Shifman, Julia M.

    2014-01-01

    Protein-protein interactions (PPI) in nature are conveyed by a multitude of binding modes involving various surfaces, secondary structure elements and intermolecular interactions. This diversity results in PPI binding affinities that span more than nine orders of magnitude. Several early studies attempted to correlate PPI binding affinities to various structure-derived features with limited success. The growing number of high-resolution structures, the appearance of more precise methods for measuring binding affinities and the development of new computational algorithms enable more thorough investigations in this direction. Here, we use a large dataset of PPI structures with the documented binding affinities to calculate a number of structure-based features that could potentially define binding energetics. We explore how well each calculated biophysical feature alone correlates with binding affinity and determine the features that could be used to distinguish between high-, medium- and low- affinity PPIs. Furthermore, we test how various combinations of features could be applied to predict binding affinity and observe a slow improvement in correlation as more features are incorporated into the equation. In addition, we observe a considerable improvement in predictions if we exclude from our analysis low-resolution and NMR structures, revealing the importance of capturing exact intermolecular interactions in our calculations. Our analysis should facilitate prediction of new interactions on the genome scale, better characterization of signaling networks and design of novel binding partners for various target proteins. PMID:25329579

  3. Fast interactive elastic registration of 12-bit multi-spectral images with subvoxel accuracy using display hardware

    NASA Astrophysics Data System (ADS)

    Noordmans, Herke Jan; de Roode, Rowland; Verdaasdonk, Rudolf

    2007-03-01

    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.

  4. Improvement of registration accuracy in accelerated partial breast irradiation using the point-based rigid-body registration algorithm for patients with implanted fiducial markers

    SciTech Connect

    Inoue, Minoru; Yoshimura, Michio Sato, Sayaka; Nakamura, Mitsuhiro; Yamada, Masahiro; Hirata, Kimiko; Ogura, Masakazu; Hiraoka, Masahiro; Sasaki, Makoto; Fujimoto, Takahiro

    2015-04-15

    Purpose: To investigate image-registration errors when using fiducial markers with a manual method and the point-based rigid-body registration (PRBR) algorithm in accelerated partial breast irradiation (APBI) patients, with accompanying fiducial deviations. Methods: Twenty-two consecutive patients were enrolled in a prospective trial examining 10-fraction APBI. Titanium clips were implanted intraoperatively around the seroma in all patients. For image-registration, the positions of the clips in daily kV x-ray images were matched to those in the planning digitally reconstructed radiographs. Fiducial and gravity registration errors (FREs and GREs, respectively), representing resulting misalignments of the edge and center of the target, respectively, were compared between the manual and algorithm-based methods. Results: In total, 218 fractions were evaluated. Although the mean FRE/GRE values for the manual and algorithm-based methods were within 3 mm (2.3/1.7 and 1.3/0.4 mm, respectively), the percentages of fractions where FRE/GRE exceeded 3 mm using the manual and algorithm-based methods were 18.8%/7.3% and 0%/0%, respectively. Manual registration resulted in 18.6% of patients with fractions of FRE/GRE exceeding 5 mm. The patients with larger clip deviation had significantly more fractions showing large FRE/GRE using manual registration. Conclusions: For image-registration using fiducial markers in APBI, the manual registration results in more fractions with considerable registration error due to loss of fiducial objectivity resulting from their deviation. The authors recommend the PRBR algorithm as a safe and effective strategy for accurate, image-guided registration and PTV margin reduction.

  5. Accuracy of surface registration compared to conventional volumetric registration in patient positioning for head-and-neck radiotherapy: A simulation study using patient data

    SciTech Connect

    Kim, Youngjun; Li, Ruijiang; Na, Yong Hum; Xing, Lei; Lee, Rena

    2014-12-15

    Purpose: 3D optical surface imaging has been applied to patient positioning in radiation therapy (RT). The optical patient positioning system is advantageous over conventional method using cone-beam computed tomography (CBCT) in that it is radiation free, frameless, and is capable of real-time monitoring. While the conventional radiographic method uses volumetric registration, the optical system uses surface matching for patient alignment. The relative accuracy of these two methods has not yet been sufficiently investigated. This study aims to investigate the theoretical accuracy of the surface registration based on a simulation study using patient data. Methods: This study compares the relative accuracy of surface and volumetric registration in head-and-neck RT. The authors examined 26 patient data sets, each consisting of planning CT data acquired before treatment and patient setup CBCT data acquired at the time of treatment. As input data of surface registration, patient’s skin surfaces were created by contouring patient skin from planning CT and treatment CBCT. Surface registration was performed using the iterative closest points algorithm by point–plane closest, which minimizes the normal distance between source points and target surfaces. Six degrees of freedom (three translations and three rotations) were used in both surface and volumetric registrations and the results were compared. The accuracy of each method was estimated by digital phantom tests. Results: Based on the results of 26 patients, the authors found that the average and maximum root-mean-square translation deviation between the surface and volumetric registrations were 2.7 and 5.2 mm, respectively. The residual error of the surface registration was calculated to have an average of 0.9 mm and a maximum of 1.7 mm. Conclusions: Surface registration may lead to results different from those of the conventional volumetric registration. Only limited accuracy can be achieved for patient

  6. PCA-based groupwise image registration for quantitative MRI.

    PubMed

    Huizinga, W; Poot, D H J; Guyader, J-M; Klaassen, R; Coolen, B F; van Kranenburg, M; van Geuns, R J M; Uitterdijk, A; Polfliet, M; Vandemeulebroucke, J; Leemans, A; Niessen, W J; Klein, S

    2016-04-01

    Quantitative magnetic resonance imaging (qMRI) is a technique for estimating quantitative tissue properties, such as the T1 and T2 relaxation times, apparent diffusion coefficient (ADC), and various perfusion measures. This estimation is achieved by acquiring multiple images with different acquisition parameters (or at multiple time points after injection of a contrast agent) and by fitting a qMRI signal model to the image intensities. Image registration is often necessary to compensate for misalignments due to subject motion and/or geometric distortions caused by the acquisition. However, large differences in image appearance make accurate image registration challenging. In this work, we propose a groupwise image registration method for compensating misalignment in qMRI. The groupwise formulation of the method eliminates the requirement of choosing a reference image, thus avoiding a registration bias. The method minimizes a cost function that is based on principal component analysis (PCA), exploiting the fact that intensity changes in qMRI can be described by a low-dimensional signal model, but not requiring knowledge on the specific acquisition model. The method was evaluated on 4D CT data of the lungs, and both real and synthetic images of five different qMRI applications: T1 mapping in a porcine heart, combined T1 and T2 mapping in carotid arteries, ADC mapping in the abdomen, diffusion tensor mapping in the brain, and dynamic contrast-enhanced mapping in the abdomen. Each application is based on a different acquisition model. The method is compared to a mutual information-based pairwise registration method and four other state-of-the-art groupwise registration methods. Registration accuracy is evaluated in terms of the precision of the estimated qMRI parameters, overlap of segmented structures, distance between corresponding landmarks, and smoothness of the deformation. In all qMRI applications the proposed method performed better than or equally well as

  7. PCA-based groupwise image registration for quantitative MRI.

    PubMed

    Huizinga, W; Poot, D H J; Guyader, J-M; Klaassen, R; Coolen, B F; van Kranenburg, M; van Geuns, R J M; Uitterdijk, A; Polfliet, M; Vandemeulebroucke, J; Leemans, A; Niessen, W J; Klein, S

    2016-04-01

    Quantitative magnetic resonance imaging (qMRI) is a technique for estimating quantitative tissue properties, such as the T1 and T2 relaxation times, apparent diffusion coefficient (ADC), and various perfusion measures. This estimation is achieved by acquiring multiple images with different acquisition parameters (or at multiple time points after injection of a contrast agent) and by fitting a qMRI signal model to the image intensities. Image registration is often necessary to compensate for misalignments due to subject motion and/or geometric distortions caused by the acquisition. However, large differences in image appearance make accurate image registration challenging. In this work, we propose a groupwise image registration method for compensating misalignment in qMRI. The groupwise formulation of the method eliminates the requirement of choosing a reference image, thus avoiding a registration bias. The method minimizes a cost function that is based on principal component analysis (PCA), exploiting the fact that intensity changes in qMRI can be described by a low-dimensional signal model, but not requiring knowledge on the specific acquisition model. The method was evaluated on 4D CT data of the lungs, and both real and synthetic images of five different qMRI applications: T1 mapping in a porcine heart, combined T1 and T2 mapping in carotid arteries, ADC mapping in the abdomen, diffusion tensor mapping in the brain, and dynamic contrast-enhanced mapping in the abdomen. Each application is based on a different acquisition model. The method is compared to a mutual information-based pairwise registration method and four other state-of-the-art groupwise registration methods. Registration accuracy is evaluated in terms of the precision of the estimated qMRI parameters, overlap of segmented structures, distance between corresponding landmarks, and smoothness of the deformation. In all qMRI applications the proposed method performed better than or equally well as

  8. Nonrigid 2D registration of fluoroscopic coronary artery image sequence with layered motion

    NASA Astrophysics Data System (ADS)

    Park, Taewoo; Jung, Hoyup; Yun, Il Dong

    2016-03-01

    We present a new method for nonrigid registration of coronary artery models with layered motion information. 2D nonrigid registration method is proposed that brings layered motion information into correspondence with fluoroscopic angiograms. The registered model is overlaid on top of interventional angiograms to provide surgical assistance during image-guided chronic total occlusion procedures. The proposed methodology is divided into two parts: layered structures alignments and local nonrigid registration. In the first part, inpainting method is used to estimate a layered rigid transformation that aligns layered motion information. In the second part, a nonrigid registration method is implemented and used to compensate for any local shape discrepancy. Experimental evaluation conducted on a set of 7 fluoroscopic angiograms results in a reduced target registration error, which showed the effectiveness of the proposed method over single layered approach.

  9. Fundus image registration for vestibularis research

    NASA Astrophysics Data System (ADS)

    Ithapu, Vamsi K.; Fritsche, Armin; Oppelt, Ariane; Westhofen, Martin; Deserno, Thomas M.

    2010-03-01

    In research on vestibular nerve disorders, fundus images of both left and right eyes are acquired systematically to precisely assess the rotation of the eye ball that is induced by the rotation of entire head. The measurement is still carried out manually. Although various methods have been proposed for medical image registration, robust detection of rotation especially in images with varied quality in terms of illumination, aberrations, blur and noise still is challenging. This paper evaluates registration algorithms operating on different levels of semantics: (i) data-based using Fourier transform and log polar maps; (ii) point-based using scaled image feature transform (SIFT); (iii) edge-based using Canny edge maps; (iv) object-based using matched filters for vessel detection; (v) scene-based detecting papilla and macula automatically and (vi) manually by two independent medical experts. For evaluation, a database of 22 patients is used, where each of left and right eye images is captured in upright head position and in lateral tilt of +/-200. For 66 pairs of images (132 in total), the results are compared with ground truth, and the performance measures are tabulated. Best correctness of 89.3% were obtained using the pixel-based method and allowing 2.5° deviation from the manual measures. However, the evaluation shows that for applications in computer-aided diagnosis involving a large set of images with varied quality, like in vestibularis research, registration methods based on a single level of semantics are not sufficiently robust. A multi-level semantics approach will improve the results since failure occur on different images.

  10. A simple method to recover Norovirus from fresh produce with large sample size by using histo-blood group antigen-conjugated to magnetic beads in a recirculating affinity magnetic separation system (RCAMS).

    PubMed

    Tian, Peng; Yang, David; Mandrell, Robert

    2011-06-30

    Human norovirus (NoV) outbreaks are major food safety concerns. The virus has to be concentrated from food samples in order to be detected. PEG precipitation is the most common method to recover the virus. Recently, histo-blood group antigens (HBGA) have been recognized as receptors for human NoV, and have been utilized as an alternative method to concentrate human NoV for samples up to 40 mL in volume. However, to wash off the virus from contaminated fresh food samples, at least 250 mL of wash volume is required. Recirculating affinity magnetic separation system (RCAMS) has been tried by others to concentrate human NoV from large-volume samples and failed to yield consistent results with the standard procedure of 30 min of recirculation at the default flow rate. Our work here demonstrates that proper recirculation time and flow rate are key factors for success in using the RCAMS. The bead recovery rate was increased from 28% to 47%, 67% and 90% when recirculation times were extended from 30 min to 60 min, 120 min and 180 min, respectively. The kinetics study suggests that at least 120 min recirculation is required to obtain a good recovery of NoV. In addition, different binding and elution conditions were compared for releasing NoV from inoculated lettuce. Phosphate-buffered saline (PBS) and water results in similar efficacy for virus release, but the released virus does not bind to RCAMS effectively unless pH was adjusted to acidic. Either citrate-buffered saline (CBS) wash, or water wash followed by CBS adjustment, resulted in an enhanced recovery of virus. We also demonstrated that the standard curve generated from viral RNA extracted from serially-diluted virus samples is more accurate for quantitative analysis than standard curves generated from serially-diluted plasmid DNA or transcribed-RNA templates, both of which tend to overestimate the concentration power. The efficacy of recovery of NoV from produce using RCAMS was directly compared with that of the

  11. 32 CFR 1615.3 - Registration procedures.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM ADMINISTRATION OF REGISTRATION § 1615.3 Registration procedures. Persons required by selective service law and the Proclamation... of Selective Service....

  12. 32 CFR 1615.3 - Registration procedures.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM ADMINISTRATION OF REGISTRATION § 1615.3 Registration procedures. Persons required by selective service law and the Proclamation... of Selective Service....

  13. 32 CFR 1615.3 - Registration procedures.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM ADMINISTRATION OF REGISTRATION § 1615.3 Registration procedures. Persons required by selective service law and the Proclamation... of Selective Service....

  14. 32 CFR 1615.3 - Registration procedures.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM ADMINISTRATION OF REGISTRATION § 1615.3 Registration procedures. Persons required by selective service law and the Proclamation... of Selective Service....

  15. 32 CFR 1615.3 - Registration procedures.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM ADMINISTRATION OF REGISTRATION § 1615.3 Registration procedures. Persons required by selective service law and the Proclamation... of Selective Service....

  16. Configurable automatic detection and registration of fiducial frames for device-to-image registration in MRI-guided prostate interventions.

    PubMed

    Tokuda, Junichi; Song, Sang-Eun; Tuncali, Kemal; Tempany, Clare; Hata, Nobuhiko

    2013-01-01

    We propose a novel automatic fiducial frame detection and registration method for device-to-image registration in MRI-guided prostate interventions. The proposed method does not require any manual selection of markers, and can be applied to a variety of fiducial frames, which consist of multiple cylindrical MR-visible markers placed in different orientations. The key idea is that automatic extraction of linear features using a line filter is more robust than that of bright spots by thresholding; by applying a line set registration algorithm to the detected markers, the frame can be registered to the MRI. The method was capable of registering the fiducial frame to the MRI with an accuracy of 1.00 +/- 0.73 mm and 1.41 +/- 1.06 degrees in a phantom study, and was sufficiently robust to detect the fiducial frame in 98% of images acquired in clinical cases despite the existence of anatomical structures in the field of view.

  17. Analytic differential approach for robust registration of rat brain histological images.

    PubMed

    Hsu, Wei-Yen

    2011-06-01

    Image registration is an important topic in medical image analysis. It is usually used to reconstruct 3D structure of tissues from a series of microscopic images. However, a variety of inherent factors may result in great differences between acquired slices during imaging even if they are adjacent. The common differences include the color difference and geometry discrepancy, which make the registration problem a difficult challenge. In this study, we propose a robust registration method to automatically reconstruct 3D volume data of the rat brain. It mainly consists of three procedures, including multiscale wavelet-based feature extraction, analytic robust point matching (ARPM), and registration refinement with feature-based modified Levenberg-Marquardt algorithm (FMLM). The product of gradient moduli in multi-scales is used to decide if extracted feature points are true according to the characteristic that features could exist in multiscale. The ARPM registration algorithm is proposed to speedily accomplish the registration of two point sets with different size by simultaneously evaluating the spatial correspondence and geometrical transformation. In addition, a FMLM method is also proposed to further refine registration results and achieve subpixel accuracy. The FMLM method converges much faster than most other methods due to its feature-based and nonlinear characteristic. The performance of proposed method is evaluated by comparing it with well-known thin-plate spline robust point matching (TPS-RPM) algorithm. The results indicate that ARPM-FMLM algorithm is a robust and fast method in image registration. PMID:20945464

  18. USDA registration and rectification requirements

    NASA Technical Reports Server (NTRS)

    Allen, R.

    1982-01-01

    Some of the requirements of the United States Department of Agriculture for accuracy of aerospace acquired data, and specifically, requirements for registration and rectification of remotely sensed data are discussed. Particular attention is given to foreign and domestic crop estimation and forecasting, forestry information applications, and rangeland condition evaluations.

  19. 21 CFR 710.6 - Notification of registrant; cosmetic product establishment registration number.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Notification of registrant; cosmetic product... OF HEALTH AND HUMAN SERVICES (CONTINUED) COSMETICS VOLUNTARY REGISTRATION OF COSMETIC PRODUCT ESTABLISHMENTS § 710.6 Notification of registrant; cosmetic product establishment registration number....

  20. 21 CFR 710.6 - Notification of registrant; cosmetic product establishment registration number.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Notification of registrant; cosmetic product... OF HEALTH AND HUMAN SERVICES (CONTINUED) COSMETICS VOLUNTARY REGISTRATION OF COSMETIC PRODUCT ESTABLISHMENTS § 710.6 Notification of registrant; cosmetic product establishment registration number....