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Anatomy Research International
Volume 2011 (2011), Article ID 287860, 17 pages
Research Article

Slice-to-Volume Nonrigid Registration of Histological Sections to MR Images of the Human Brain

1Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
2204 Rockwell Engineering Center, University of California, Irvine, CA 92697-2755, USA

Received 15 June 2010; Revised 12 August 2010; Accepted 8 September 2010

Academic Editor: Feng C. Zhou

Copyright © 2011 Sergey Osechinskiy and Frithjof Kruggel. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Registration of histological images to three-dimensional imaging modalities is an important step in quantitative analysis of brain structure, in architectonic mapping of the brain, and in investigation of the pathology of a brain disease. Reconstruction of histology volume from serial sections is a well-established procedure, but it does not address registration of individual slices from sparse sections, which is the aim of the slice-to-volume approach. This study presents a flexible framework for intensity-based slice-to-volume nonrigid registration algorithms with a geometric transformation deformation field parametrized by various classes of spline functions: thin-plate splines (TPS), Gaussian elastic body splines (GEBS), or cubic B-splines. Algorithms are applied to cross-modality registration of histological and magnetic resonance images of the human brain. Registration performance is evaluated across a range of optimization algorithms and intensity-based cost functions. For a particular case of histological data, best results are obtained with a TPS three-dimensional (3D) warp, a new unconstrained optimization algorithm (NEWUOA), and a correlation-coefficient-based cost function.