MRI-guided volume reconstruction of mouse brain from histological sections

Yang, Zhengyi, Richards, Kay, Kurniawan, Nyoman D., Petrou, Steven and Reutens, David C. (2012) MRI-guided volume reconstruction of mouse brain from histological sections. Journal of Neuroscience Methods, 211 2: 2010-2017. doi:10.1016/j.jneumeth.2012.08.021

Author Yang, Zhengyi
Richards, Kay
Kurniawan, Nyoman D.
Petrou, Steven
Reutens, David C.
Total Author Count Override 5
Title MRI-guided volume reconstruction of mouse brain from histological sections
Journal name Journal of Neuroscience Methods   Check publisher's open access policy
ISSN 0165-0270
Publication date 2012-11-15
Sub-type Article (original research)
DOI 10.1016/j.jneumeth.2012.08.021
Volume 211
Issue 2
Start page 2010
End page 2017
Total pages 8
Place of publication Amsterdam, Netherlands
Publisher Elsevier
Collection year 2013
Language eng
Abstract A method is presented for three-dimensional reconstruction of the mouse brain from histological sections with the guidance of magnetic resonance images (MRI). A major focus of the method is dealing with sections in which anatomical structures have been separated or distorted as a result of histological processing. Although histology has superb resolution with the ability to discriminate cell types and anatomical structures, misalignment between sections and distortion within sections renders 3D reconstruction of the histology volume simply by stacking 2D sections inadequate. In contrast, MRI preserves the spatial and geometric information about structures at a cost of cellular detail. To utilize the information from MRI in reconstructing volumetric histological data, we developed a procedure consisting of a series of segmentation and registration operations. The method is iterative and first identifies the corresponding MRI slices for each histological section. Piecewise rigid registration is then employed to deal with tissue distortion caused by histological processing. Quantitative validation of the method's accuracy was performed on four reconstructed mouse brains by comparing a set of manually selected anatomical landmarks on pairs of MRI and histological volumes. The procedure is highly automated and amenable to high throughput.
Keyword Histology reconstruction
Magnetic resonance image
Piecewise rigid registration
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2013 Collection
Centre for Advanced Imaging Publications
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Created: Tue, 30 Oct 2012, 16:43:15 EST by Sandrine Ducrot on behalf of Centre for Advanced Imaging