CONFERENCE PROCEEDINGS
Advanced Search
Home > Journals > Neurophoton. > Volume 4 > Issue 4 > Article
Open Access
11 July 2017 Whole mouse brain imaging using optical coherence tomography: reconstruction, normalization, segmentation, and comparison with diffusion MRI
Joël Lefebvre, Alexandre Castonguay, Philippe Pouliot, Maxime Descoteaux, Frédéric Lesage
Author Affiliations +
Neurophotonics, Vol. 4, Issue 4, 041501 (July 2017). https://doi.org/10.1117/1.NPh.4.4.041501
Abstract
An automated massive histology setup combined with an optical coherence tomography (OCT) microscope was used to image a total of n=5 whole mouse brains. Each acquisition generated a dataset of thousands of OCT volumetric tiles at a sampling resolution of 4.9×4.9×6.5  μm. This paper describes techniques for reconstruction and segmentation of the sliced brains. In addition to the measured OCT optical reflectivity, a single scattering photon model was used to compute the attenuation coefficients within each tissue slice. Average mouse brain templates were generated for both the OCT reflectivity and attenuation contrasts and were used with an n-tissue segmentation algorithm. To better understand the brain tissue OCT contrast origin, one of the mouse brains was acquired using dMRI and coregistered to its corresponding assembled brain. Our results indicate that the optical reflectivity in a fiber bundle varies with its orientation, its fiber density, and the number of fiber orientations it contains. The OCT mouse brain template generation and coregistration to dMRI data demonstrate the potential of this massive histology technique to pursue cross-sectional, multimodal, and multisubject investigations of small animal brains.
© 2017 Society of Photo-Optical Instrumentation Engineers (SPIE) 2329-423X/2017/$25.00 © 2017 SPIE
Citation Download Citation
Joël Lefebvre, Alexandre Castonguay, Philippe Pouliot, Maxime Descoteaux, and Frédéric Lesage "Whole mouse brain imaging using optical coherence tomography: reconstruction, normalization, segmentation, and comparison with diffusion MRI," Neurophotonics 4(4), 041501 (11 July 2017). https://doi.org/10.1117/1.NPh.4.4.041501
Received: 30 March 2017; Accepted: 19 June 2017; Published: 11 July 2017
JOURNAL ARTICLE
 14 PAGES
DOWNLOAD PAPER SAVE TO MY LIBRARY
GET CITATION
Lens.org Logo
CITATIONS
Cited by 29 scholarly publications.
Advertisement
Advertisement
RIGHTS & PERMISSIONS
Get copyright permission  Get copyright permission on Copyright Marketplace
KEYWORDS
Optical coherence tomography
Brain
Image segmentation
Brain imaging
Diffusion magnetic resonance imaging
Reflectivity
Tissue optics
RELATED CONTENT
Subscribe to Digital Library
Receive Erratum Email Alert
Back to Top