Algorithms for Warping of 2-D PAGE Maps.

Software-based image analysis of 2-D PAGE maps is an important step for the investigation of proteome. Warping algorithms, which are employed to register spots among gels, are able to overcome the difficulties due to the low reproducibility of this analytical technique. Over the years, the research of new matching and warping mathematical methods has allowed the development of several routine applications of easy-to-use software. This chapter describes common and basic spatial transformations used for the alignment of protein spots present in different gel maps; some recently new approaches are also presented.

[1]  B. Walczak,et al.  Fuzzy warping of chromatograms , 2005 .

[2]  Dinggang Shen,et al.  Very High-Resolution Morphometry Using Mass-Preserving Deformations and HAMMER Elastic Registration , 2003, NeuroImage.

[3]  David J. Hawkes,et al.  Deformations Incorporating Rigid Structures , 1996, Comput. Vis. Image Underst..

[4]  M Daszykowski,et al.  Start-to-end processing of two-dimensional gel electrophoretic images. , 2007, Journal of chromatography. A.

[5]  Fred L. Bookstein,et al.  Principal Warps: Thin-Plate Splines and the Decomposition of Deformations , 1989, IEEE Trans. Pattern Anal. Mach. Intell..

[6]  Karl Rohr,et al.  A New Class of Elastic Body Splines for Nonrigid Registration of Medical Images , 2005, Journal of Mathematical Imaging and Vision.

[7]  Beata Walczak,et al.  Baseline reduction in two dimensional gel electrophoresis images , 2005 .

[8]  R. Haddad,et al.  Multiresolution Signal Decomposition: Transforms, Subbands, and Wavelets , 1992 .

[9]  D. Kell,et al.  An introduction to wavelet transforms for chemometricians: A time-frequency approach , 1997 .

[10]  Michael Unser,et al.  Elastic registration of biological images using vector-spline regularization , 2005, IEEE Transactions on Biomedical Engineering.

[11]  Hans-Hellmut Nagel,et al.  Displacement vectors derived from second-order intensity variations in image sequences , 1983, Comput. Vis. Graph. Image Process..

[12]  Roberto Marcondes Cesar Junior,et al.  Structural matching of 2D electrophoresis gels using deformed graphs , 2011, Pattern Recognit. Lett..

[13]  K. Kaczmarek,et al.  Feature Based Fuzzy Matching of 2D Gel Electrophoresis Images , 2002, J. Chem. Inf. Comput. Sci..

[14]  D. Hill,et al.  Medical image registration , 2001, Physics in medicine and biology.

[15]  Karl Rohr,et al.  Elastic registration of electrophoresis images using intensity information and point landmarks , 2004, Pattern Recognit..

[16]  S Veeser,et al.  Multiresolution image registration for two‐dimensional gel electrophoresis , 2001, Proteomics.

[17]  M Daszykowski,et al.  Target selection for alignment of chromatographic signals obtained using monochannel detectors. , 2007, Journal of chromatography. A.

[18]  George J. Klir,et al.  Fuzzy sets and fuzzy logic - theory and applications , 1995 .

[19]  K. Kaczmarek,et al.  Matching 2D Gel Electrophoresis Images , 2003, J. Chem. Inf. Comput. Sci..

[20]  I. Johnstone,et al.  Adapting to Unknown Smoothness via Wavelet Shrinkage , 1995 .

[21]  Nicholas Ayache,et al.  c ○ 2004 Kluwer Academic Publishers. Manufactured in The Netherlands. Isotropic Energies, Filters and Splines for Vector Field Regularization , 2022 .

[22]  Jan Modersitzki,et al.  Optimal Image Registration with a Guaranteed One-to-one Point Match , 2003, Bildverarbeitung für die Medizin.

[23]  George Wolberg,et al.  Digital image warping , 1990 .

[24]  Jitendra Malik,et al.  Shape matching and object recognition using shape contexts , 2010, 2010 3rd International Conference on Computer Science and Information Technology.

[25]  D. Louis Collins,et al.  Non-linear Cerebral Registration with Sulcal Constraints , 1998, MICCAI.

[26]  Alon Efrat,et al.  Geometric Algorithms for the Analysis of 2D-Electrophoresis Gels , 2002, J. Comput. Biol..

[27]  Anand Rangarajan,et al.  A new algorithm for non-rigid point matching , 2000, Proceedings IEEE Conference on Computer Vision and Pattern Recognition. CVPR 2000 (Cat. No.PR00662).

[28]  Bruno Josso,et al.  Automatic 2-D gel registration using distance minimisation of image morphing , 2000, 2000 IEEE Conference on Information Visualization. An International Conference on Computer Visualization and Graphics.

[29]  K Rohr,et al.  Geometric alignment of 2D gel electrophoresis images. , 2009, Methods of information in medicine.

[30]  Konagaya,et al.  Automated Processing of 2-D Gel Electrophoretograms of Genomic DNA for Hunting Pathogenic DNA Molecular Changes. , 1999, Genome informatics. Workshop on Genome Informatics.

[31]  Tianzi Jiang,et al.  Alignment of two-dimensional electrophoresis gels. , 2007, Biochemical and biophysical research communications.

[32]  Roberto Marcondes Cesar Junior,et al.  Inexact graph matching for model-based recognition: Evaluation and comparison of optimization algorithms , 2005, Pattern Recognit..

[33]  Beata Walczak,et al.  Matching 2D gel electrophoresis images with Matlab ‘Image Processing Toolbox’ , 2009 .

[34]  Richard Sinkhorn.  A Relationship Between Arbitrary Positive Matrices and Doubly Stochastic Matrices , 1964 .

[35]  J I Garrels,et al.  Two dimensional gel electrophoresis and computer analysis of proteins synthesized by clonal cell lines. , 1979, The Journal of biological chemistry.

[36]  Babu Raman,et al.  Quantitative comparison and evaluation of two commercially available, two‐dimensional electrophoresis image analysis software packages, Z3 and Melanie , 2002, Electrophoresis.

[37]  X. Pennec,et al.  3D non-rigid registration by gradient descent on a Gaussian-windowed similarity measure using convolutions , 2000, Proceedings IEEE Workshop on Mathematical Methods in Biomedical Image Analysis. MMBIA-2000 (Cat. No.PR00737).

[38]  Jelena Kovacevic,et al.  Wavelets and Subband Coding , 2013, Prentice Hall Signal Processing Series.

[39]  Brian Fenton,et al.  Superimposing two‐dimensional gels to study genetic variation in malaria parasites , 1992, Electrophoresis.

[40]  Haiying Liu,et al.  Using Points and Surfaces to Improve Voxel-Based Non-rigid Registration , 2002, MICCAI.

[41]  P. Lemkin.  Comparing two‐dimensional electrophoretic gel images across the Internet , 1997, Electrophoresis.

[42]  Mark Berman.  Automated Smoothing of Image and Other Regularly Spaced Data , 1994, IEEE Trans. Pattern Anal. Mach. Intell..

[43]  Simon R. Arridge,et al.  A survey of hierarchical non-linear medical image registration , 1999, Pattern Recognit..

[44]  Magni Martens,et al.  Multivariate Analysis of Quality : An Introduction , 2001 .

[45]  Richard Szeliski,et al.  Motion Estimation with Quadtree Splines , 1996, IEEE Trans. Pattern Anal. Mach. Intell..

[46]  G. Strang.  Wavelet transforms versus Fourier transforms , 1993, math/9304214.

[47]  Beata Walczak,et al.  Pixel‐based analysis of multiple images for the identification of changes: A novel approach applied to unravel proteome patters of 2‐D electrophoresis gel images , 2007 .

[48]  Julian Magarey,et al.  Optimal schemes for motion estimation on colour image sequences , 1997, Proceedings of International Conference on Image Processing.

[49]  Ingrid Daubechies,et al.  Ten Lectures on Wavelets , 1992 .

[50]  Michael Unser,et al.  A pyramid approach to subpixel registration based on intensity , 1998, IEEE Trans. Image Process..

[51]  Jim Graham,et al.  Robust and Accurate Registration of 2-D Electrophoresis Gels Using Point-Matching , 2007, IEEE Transactions on Image Processing.

[52]  Gerald Q. Maguire,et al.  Comparison and evaluation of retrospective intermodality brain image registration techniques. , 1997, Journal of computer assisted tomography.

[53]  Helmut E Meyer,et al.  Examination of 2‐DE in the Human Proteome Organisation Brain Proteome Project pilot studies with the new RAIN gel matching technique , 2006, Proteomics.

[54]  Chandra Kambhamettu,et al.  An image analysis suite for spot detection and spot matching in two‐dimensional electrophoresis gels , 2008, Electrophoresis.

[55]  Tadao Asami,et al.  Adaptation of Restriction Landmark Genomic Scanning (RLGS) to plant genome analysis , 2000, Plant Molecular Biology Reporter.

[56]  Yuan Yan Tang,et al.  Image transformation approach to nonlinear shape restoration , 1993, IEEE Trans. Syst. Man Cybern..

[57]  Beata Walczak,et al.  Comparison of image-transformation methods used in matching 2D gel electrophoresis images , 2003 .

[58]  Martin Vogt,et al.  Automatic registration and segmentation algorithm for multiple electrophoresis images , 2000, Medical Imaging: Image Processing.

[59]  Daniel Rueckert,et al.  Nonrigid registration using free-form deformations: application to breast MR images , 1999, IEEE Transactions on Medical Imaging.

[60]  K. Mardia,et al.  A penalized likelihood approach to image warping , 2001 .

[61]  Gary E. Christensen,et al.  Consistent landmark and intensity-based image registration , 2002, IEEE Transactions on Medical Imaging.

[62]  Paul J. Besl,et al.  A Method for Registration of 3-D Shapes , 1992, IEEE Trans. Pattern Anal. Mach. Intell..

[63]  Carlos Fernandez-Lozano,et al.  Two-dimensional gel electrophoresis image registration using block-matching techniques and deformation models. , 2014, Analytical biochemistry.

[64]  Philip E. Gill,et al.  Practical optimization , 1981 .

[65]  Julian Magarey,et al.  An improved motion estimation algorithm using complex wavelets , 1996, Proceedings of 3rd IEEE International Conference on Image Processing.

[66]  Nicholas Ayache,et al.  Unifying maximum likelihood approaches in medical image registration , 2000 .

[67]  Andrew M Woodward,et al.  Fast automatic registration of images using the phase of a complex wavelet transform: application to proteome gels. , 2004, The Analyst.

[68]  Yali Amit,et al.  A Nonlinear Variational Problem for Image Matching , 1994, SIAM J. Sci. Comput..

[69]  Karl Rohr,et al.  Physics-based elastic registration using non-radial basis functions and including landmark localization uncertainties , 2008, Comput. Vis. Image Underst..

[70]  Kelvin H Lee,et al.  Quantitative and qualitative measure of intralaboratory two‐dimensional protein gel reproducibility and the effects of sample preparation, sample load, and image analysis , 2003, Electrophoresis.

[71]  Guang-Zhong Yang,et al.  Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline , 2008, Bioinform..

[72]  Watanabe,et al.  Fully-Automated Spot Recognition and Matching Algorithms for 2-D Gel Electrophoretogram of Genomic DNA. , 1998, Genome informatics. Workshop on Genome Informatics.

[73]  Pierre Hellier,et al.  Cooperation between Local and Global Approaches to Register Brain Images , 2001, IPMI.

[74]  Jean-Luc Starck,et al.  Image Processing and Data Analysis: Geometric registration , 1998 .

[75]  Katsuhiko Sakaue,et al.  Registration and integration of multiple range images for 3-D model construction , 1996, Proceedings of 13th International Conference on Pattern Recognition.

[76]  K. Mardia,et al.  A review of image-warping methods , 1998 .

[77]  Lawrence H. Staib,et al.  Elastic Model Based Non-rigid Registration Incorporation Statistical Shape Information , 1998, MICCAI.

[78]  G. Wahba.  How to Smooth Curves and Surfaces with Splines and Cross-Validation , 1979 .

[79]  Julian Magarey,et al.  Motion estimation using a complex-valued wavelet transform , 1998, IEEE Trans. Signal Process..

[80]  R D Appel,et al.  Melanie II – a third‐generation software package for analysis of two‐dimensional electrophoresis images: II. Algorithms , 1997, Electrophoresis.

[81]  Marina Cocchi,et al.  GENOCOP algorithm and hierarchical grid transformation for image warping of two dimensional gel eletrophoretic maps. , 2012, Molecular bioSystems.

[82]  Ellis Horowitz,et al.  Fundamentals of data structures in C , 1976 .

[83]  A. Mahadevan-Jansen,et al.  Automated Method for Subtraction of Fluorescence from Biological Raman Spectra , 2003, Applied spectroscopy.

[84]  Daw-Tung Lin,et al.  Autonomous sub-image matching for two-dimensional electrophoresis gels using MaxRST algorithm , 2010, Image Vis. Comput..

[85]  Z. Smilansky,et al.  Automatic registration for images of two‐dimensional protein gels , 2001, Electrophoresis.

[86]  King-Sun Fu,et al.  Error-Correcting Isomorphisms of Attributed Relational Graphs for Pattern Analysis , 1979, IEEE Transactions on Systems, Man, and Cybernetics.

[87]  I. J. Schoenberg.  Contributions to the problem of approximation of equidistant data by analytic functions. Part A. On the problem of smoothing or graduation. A first class of analytic approximation formulae , 1946 .

[88]  P F Lemkin,et al.  GELLAB: A computer system for 2D gel electrophoresis analysis. II. Pairing spots. , 1981, Computers and biomedical research, an international journal.

[89]  Horst Bunke,et al.  On a relation between graph edit distance and maximum common subgraph , 1997, Pattern Recognit. Lett..

[90]  Jean-Francois Mangin,et al.  Multisubject Non-rigid Registration of Brain MRI Using Intensity and Geometric Features , 2001, MICCAI.

[91]  David Dagan Feng,et al.  Hybrid registration for two-dimensional gel protein images , 2005, APBC.

[92]  Stéphane Mallat,et al.  A Theory for Multiresolution Signal Decomposition: The Wavelet Representation , 1989, IEEE Trans. Pattern Anal. Mach. Intell..

[93]  Paul H. C. Eilers,et al.  Fast and compact smoothing on large multidimensional grids , 2006, Comput. Stat. Data Anal..

[94]  Anders Blomberg,et al.  Warping two‐dimensional electrophoresis gel images to correct for geometric distortions of the spot pattern , 2002, Electrophoresis.

[95]  Kari Pulli,et al.  Multiview registration for large data sets , 1999, Second International Conference on 3-D Digital Imaging and Modeling (Cat. No.PR00062).

[96]  Mario Vento,et al.  Thirty Years Of Graph Matching In Pattern Recognition , 2004, Int. J. Pattern Recognit. Artif. Intell..

[97]  I. J. Schoenberg.  Contributions to the Problem of Approximation of Equidistant Data by Analytic Functions , 1988 .