White matter segmentation by estimating tissue optical attenuation from volumetric OCT massive histology of whole rodent brains

Joël Lefebvre; Alexandre Castonguay; Frédéric Lesage

doi:10.1117/12.2251173

17 February 2017 White matter segmentation by estimating tissue optical attenuation from volumetric OCT massive histology of whole rodent brains

Joël Lefebvre, Alexandre Castonguay, Frédéric Lesage

Author Affiliations +

Proceedings Volume 10070, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXIV; 1007012 (2017) https://doi.org/10.1117/12.2251173
Event: SPIE BiOS, 2017, San Francisco, California, United States

Abstract

A whole rodent brain was imaged using an automated massive histology setup and an Optical Coherence Tomography (OCT) microscope. Thousands of OCT volumetric tiles were acquired, each covering a size of about 2.5x2.5x0.8 mm3 with a sampling resolution of 4.9x4.9x6.5 microns. This paper shows the techniques for reconstruction, attenuation compensation and segmentation of the sliced brains. The tile positions within the mosaic were evaluated using a displacement model of the motorized stage and pairwise coregistration. Volume blending was then performed by solving the 3D Laplace equation, and consecutive slices were assembled using the cross-correlation of their 2D image gradient. This reconstruction algorithm resulted in a 3D map of optical reflectivity for the whole brain at micrometric resolution. OCT tissue slices were then used to estimate the local attenuation coefficient based on a single scattering photon model. The attenuation map obtained exhibits a high contrast for all white matter fibres, regardless of their orientation. The tissue optical attenuation from the intrinsic OCT reflectivity contributes to better white matter tissue segmentation. The combined 3D maps of reflectivity and attenuation is a step toward the study of white matter at a microscopic scale for the whole brain in small animals.

Citation Download Citation

Joël Lefebvre, Alexandre Castonguay, and Frédéric Lesage "White matter segmentation by estimating tissue optical attenuation from volumetric OCT massive histology of whole rodent brains", Proc. SPIE 10070, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXIV, 1007012 (17 February 2017); https://doi.org/10.1117/12.2251173

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