A mathematical model of the primary visual cortex and hypercolumn
Biological Cybernetics
Registration of Translated and Rotated Images Using Finite Fourier Transforms
IEEE Transactions on Pattern Analysis and Machine Intelligence
Hierarchical Chamfer Matching: A Parametric Edge Matching Algorithm
IEEE Transactions on Pattern Analysis and Machine Intelligence
Principal Warps: Thin-Plate Splines and the Decomposition of Deformations
IEEE Transactions on Pattern Analysis and Machine Intelligence
Multiresolution elastic matching
Computer Vision, Graphics, and Image Processing
An adaptive multigrid technique for the incompressible Navier-Stokes equations
Journal of Computational Physics
Machine Vision and Applications - Special issue: Three-dimensional microscopy
A survey of image registration techniques
ACM Computing Surveys (CSUR)
A parallel multigrid algorithm for solving the Navier-Stokes equations
IMPACT of Computing in Science and Engineering
Spatial transformation and registration of brain images using elastically deformable models
Computer Vision and Image Understanding
Alignment by Maximization of Mutual Information
International Journal of Computer Vision
The Handbook of Brain Theory and Neural Networks
The Handbook of Brain Theory and Neural Networks
Elastic Matching of Very Large Digital Images on High Performance Clusters
HPCN Europe '99 Proceedings of the 7th International Conference on High-Performance Computing and Networking
Registration of Reconstructed Post Mortem Optical Data with MR Scans of the Same Patient
MICCAI '01 Proceedings of the 4th International Conference on Medical Image Computing and Computer-Assisted Intervention
MICCAI '98 Proceedings of the First International Conference on Medical Image Computing and Computer-Assisted Intervention
MICCAI '01 Proceedings of the 4th International Conference on Medical Image Computing and Computer-Assisted Intervention
Deformable Organisms for Automatic Medical Image Analysis
MICCAI '01 Proceedings of the 4th International Conference on Medical Image Computing and Computer-Assisted Intervention
MICCAI '01 Proceedings of the 4th International Conference on Medical Image Computing and Computer-Assisted Intervention
A New Approach to Fast Elastic Alignment with Applications to Human Brain
VBC '96 Proceedings of the 4th International Conference on Visualization in Biomedical Computing
Extension of the Principle Axes Theory for the Determination of Affine Transformation
Mustererkennung 1997, 19. DAGM-Symposium
Fast Fluid Registration of Medical Images
VBC '96 Proceedings of the 4th International Conference on Visualization in Biomedical Computing
Alignment by maximization of mutual information
ICCV '95 Proceedings of the Fifth International Conference on Computer Vision
Optimal registration of deformed images
Optimal registration of deformed images
Genetic algorithms for a robust 3-D MR-CT registration
IEEE Transactions on Information Technology in Biomedicine
Landmark matching via large deformation diffeomorphisms
IEEE Transactions on Image Processing
An automatic nonrigid registration for stained histological sections
IEEE Transactions on Image Processing
Non-rigid Registration for Large Sets of Microscopic Images on Graphics Processors
Journal of Signal Processing Systems
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Technical Section: CGV-An interactive graph visualization system
Computers and Graphics
Reconstruction of 3-D histology images by simultaneous deformable registration
MICCAI'11 Proceedings of the 14th international conference on Medical image computing and computer-assisted intervention - Volume Part II
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The physical (microtomy), optical (microscopy), and radiologic (tomography) sectioning of biological objects and their digitization lead to stacks of images. Due to the sectioning process and disturbances, movement of objects during imaging for example, adjacent images of the image stack are not optimally aligned to each other. Such mismatches have to be corrected automatically by suitable registration methods.Here, a whole brain of a Sprague Dawley rat was serially sectioned and stained followed by digitizing the 20 驴m thin histologic sections. We describe how to prepare the images for subsequent automatic intensity based registration. Different registration schemes are presented and their results compared to each other from an anatomical and mathematical perspective. In the first part we concentrate on rigid and affine linear methods and deal only with linear mismatches of the images. Digitized images of stained histologic sections often exhibit inhomogenities of the gray level distribution coming from staining and/or sectioning variations. Therefore, a method is developed that is robust with respect to inhomogenities and artifacts. Furthermore we combined this approach by minimizing a suitable distance measure for shear and rotation mismatches of foreground objects after applying the principal axes transform. As a consequence of our investigations, we must emphasize that the combination of a robust principal axes based registration in combination with optimizing translation, rotation and shearing errors gives rise to the best reconstruction results from the mathematical and anatomical view point.Because the sectioning process introduces nonlinear deformations to the relative thin histologic sections as well, an elastic registration has to be applied to correct these deformations.In the second part of the study a detailed description of the advances of an elastic registration after affine linear registration of the rat brain is given. We found quantitative evidence that affine linear registration is a suitable starting point for the alignment of histologic sections but elastic registration must be performed to improve significantly the registration result. A strategy is presented that enables to register elastically the affine linear preregistered~ rat brain sections and the first one hundred images of serial histologic sections through both occipital lobes of a human brain (6112 images). Additionally, we will describe how a parallel implementation of the elastic registration was realized. Finally, the computed force fields have been applied here for the first time to the morphometrized data of cells determined automatically by an image analytic framework.