Group-wise 3D MR Image Registration of Mouse Embryos

This dissertation provides the foundations of computer-based automated phenotyping methods for analyzing 3D images of mouse embryos. A group-wise registration technique was utilized and optimized and computerized methods were employed for analysis of 3D MRI images of mouse embryos. The assumption that embryo anatomy is highly conserved among genetically identical specimens was verified. The group-wise registration approach was used to align a group of embryos from the 129S1/SvImJ (129Sv) strain as well as a group of C57BL/6J (C57) embryos. Finally, we shed some light on some of the morphological differences between the 129Sv and C57 strains using automated techniques.

[1]  David J. Hawkes,et al.  Voxel similarity measures for 3-D serial MR brain image registration , 1999, IEEE Transactions on Medical Imaging.

[2]  Roger P. Woods,et al.  Characterizing volume and surface deformations in an atlas framework: theory, applications, and implementation , 2003, NeuroImage.

[3]  Max A. Viergever,et al.  A survey of medical image registration , 1998, Medical Image Anal..

[4]  Alan C. Evans,et al.  A Unified Statistical Approach to Deformation-Based Morphometry , 2001, NeuroImage.

[5]  D. Hill,et al.  Non-rigid image registration: theory and practice. , 2004, The British journal of radiology.

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

[7]  S Lee Adamson,et al.  Embryonic and neonatal phenotyping of genetically engineered mice. , 2006, ILAR journal.

[8]  Michael R Chernick,et al.  Bootstrap Methods: A Guide for Practitioners and Researchers , 2007 .

[9]  Mark Holden,et al.  A Review of Geometric Transformations for Nonrigid Body Registration , 2008, IEEE Transactions on Medical Imaging.

[10]  Pierre Hellier,et al.  Hierarchical estimation of a dense deformation field for 3-D robust registration , 2001, IEEE Transactions on Medical Imaging.

[11]  J. Sharpe.  Optical projection tomography. , 2004, Annual review of biomedical engineering.

[12]  E. Ritman.  Micro-computed tomography-current status and developments. , 2004, Annual review of biomedical engineering.

[13]  F. A. Seiler,et al.  Numerical Recipes in C: The Art of Scientific Computing , 1989 .

[14]  R. Jacobs,et al.  Three-dimensional digital mouse atlas using high-resolution MRI. , 2001, Developmental biology.

[15]  Jan Modersitzki,et al.  Numerical Methods for Image Registration , 2004 .

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

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

[18]  Paul M. Thompson,et al.  A framework for computational anatomy , 2002 .

[19]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[20]  Guido Gerig,et al.  User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability , 2006, NeuroImage.

[21]  D. Louis Collins,et al.  Animal: Validation and Applications of Nonlinear Registration-Based Segmentation , 1997, Int. J. Pattern Recognit. Artif. Intell..

[22]  Jean Meunier,et al.  Average Brain Models: A Convergence Study , 2000, Comput. Vis. Image Underst..

[23]  Wolfgang Wurst,et al.  A Mouse for All Reasons , 2007, Cell.

[24]  Charles A. Bouman,et al.  A multiscale random field model for Bayesian image segmentation , 1994, IEEE Trans. Image Process..

[25]  Matthew H. Kaufman,et al.  The Atlas of Mouse Development , 1992 .

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

[27]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[28]  Natasa Kovacevic,et al.  Deformation Based Representation of Groupwise Average and Variability , 2004, MICCAI.

[29]  Natasa Kovacevic,et al.  Neuroanatomical differences between mouse strains as shown by high-resolution 3D MRI , 2006, NeuroImage.

[30]  J. H. Zar,et al.  Biostatistical Analysis (5th Edition) , 1984 .

[31]  R. Leahy,et al.  Magnetic Resonance Image Tissue Classification Using a Partial Volume Model , 2001, NeuroImage.

[32]  D. Louis Collins,et al.  Automatic 3‐D model‐based neuroanatomical segmentation , 1995 .

[33]  Alan C. Evans,et al.  A three-dimensional MRI atlas of the mouse brain with estimates of the average and variability. , 2005, Cerebral cortex.

[34]  Alan C. Evans,et al.  Longitudinal neuroanatomical changes determined by deformation-based morphometry in a mouse model of Alzheimer's disease , 2008, NeuroImage.

[35]  Magnetic resonance imaging analysis of embryos. , 2000, Methods in molecular biology.

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

[37]  Guido Gerig,et al.  Unbiased diffeomorphic atlas construction for computational anatomy , 2004, NeuroImage.

[38]  Paul M. Thompson,et al.  Statistical Properties of Jacobian Maps and the Realization of Unbiased Large-Deformation Nonlinear Image Registration , 2007, IEEE Transactions on Medical Imaging.

[39]  Paul M. Thompson,et al.  The role of image registration in brain mapping , 2001, Image Vis. Comput..

[40]  M. Capecchi,et al.  Virtual Histology of Transgenic Mouse Embryos for High-Throughput Phenotyping , 2006, PLoS genetics.

[41]  S. Neubauer,et al.  Identification of cardiac malformations in mice lacking Ptdsr using a novel high-throughput magnetic resonance imaging technique , 2004, BMC Developmental Biology.

[42]  J. Mazziotta,et al.  Regional Spatial Normalization: Toward an Optimal Target , 2001, Journal of computer assisted tomography.

[43]  Michael I. Miller,et al.  Deformable templates using large deformation kinematics , 1996, IEEE Trans. Image Process..

[44]  B. Hogan,et al.  Manipulating the mouse embryo: A laboratory manual , 1986 .

[45]  M. Dickinson,et al.  Multimodal imaging of mouse development: Tools for the postgenomic era , 2006, Developmental dynamics : an official publication of the American Association of Anatomists.

[46]  S Lee Adamson,et al.  In vivo quantification of embryonic and placental growth during gestation in mice using micro-ultrasound , 2008, Reproductive biology and endocrinology : RB&E.

[47]  Thomas E. Nichols,et al.  Thresholding of Statistical Maps in Functional Neuroimaging Using the False Discovery Rate , 2002, NeuroImage.

[48]  Alan C. Evans,et al.  A nonparametric method for automatic correction of intensity nonuniformity in MRI data , 1998, IEEE Transactions on Medical Imaging.

[49]  R. Mark Henkelman,et al.  In vivo multiple‐mouse MRI at 7 Tesla , 2005, Magnetic resonance in medicine.

[50]  Christos Davatzikos,et al.  Spatial Transformation and Registration of Brain Images Using Elastically Deformable Models , 1997, Comput. Vis. Image Underst..

[51]  Florence Franconi,et al.  In utero time-course assessment of mouse embryo development using high resolution magnetic resonance imaging , 2002, Anatomy and Embryology.

[52]  Stephen R. Marsland,et al.  Groupwise Non-rigid Registration Using Polyharmonic Clamped-Plate Splines , 2003, MICCAI.

[53]  Robert Tibshirani,et al.  An Introduction to the Bootstrap , 1994 .

[54]  G. Johnson,et al.  High-resolution magnetic resonance histology of the embryonic and neonatal mouse: A 4D atlas and morphologic database , 2008, Proceedings of the National Academy of Sciences.

[55]  Thomas Martin Deserno,et al.  Survey: interpolation methods in medical image processing , 1999, IEEE Transactions on Medical Imaging.

[56]  P. Kaufmann.  The anatomical basis of mouse development , 1999 .

[57]  W. Frankel,et al.  Moving forward with chemical mutagenesis in the mouse , 2004, The Journal of physiology.

[58]  D. Louis Collins,et al.  Tuning and Comparing Spatial Normalization Methods , 2003, MICCAI.

[59]  J. Mullikin,et al.  Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains , 2005, Nature Genetics.

[60]  Colin Studholme.  Simultaneous Population Based Image Alignment for Template Free Spatial Normalisation of Brain Anatomy , 2003, WBIR.

[61]  J. Ashburner,et al.  Nonlinear spatial normalization using basis functions , 1999, Human brain mapping.