Generation of a 3D atlas of the nuclear division of the thalamus based on histological sections of primate: Intra- and intersubject atlas-to-MRI warping

Abstract We describe a framework to generate a 3D digital atlas of the thalamus based on a series of stained histological sections of a primate. The contours of the thalamus were first drawn on the stained histological slices. The series of histological sections were then aligned and mapped onto the...

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Published inIngénierie et recherche biomédicale Vol. 30; no. 5; pp. 281 - 291
Main Authors Dauguet, J, Condé, F, Hantraye, P, Frouin, V, Delzescaux, T
Format Journal Article
LanguageEnglish
Published Elsevier Masson SAS 01.11.2009
Subjects
3D Reconstruction
Atlas digital
Digital Atlas
Histologie
Histology
Internal Medicine
Primate
Reconstruction 3D
Thalamus
Histologie
3D Reconstruction
Primate
Thalamus
Histology
Digital Atlas
Atlas digital
Reconstruction 3D
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Summary:Abstract We describe a framework to generate a 3D digital atlas of the thalamus based on a series of stained histological sections of a primate. The contours of the thalamus were first drawn on the stained histological slices. The series of histological sections were then aligned and mapped onto the in vivo MRI of the same animal acquired prior to the sacrifice following a methodology described in Dauguet et al. (2007) [1] using the block face photographs as an intermediary modality. By applying the series of transformations previously estimated for the histological volume, the contours of the digital atlas were mapped onto the MRI data. The protocol was tested on two baboon brains for which the full series of slices were available, and a macaque brain for which a subset only of the histological slices were available demonstrating the ability of building digital atlases in the MRI geometry without mounting and staining all the brain slices. We then studied the accuracy of mapping the digital atlas of one baboon onto the MRI of the other baboon by comparing the overlapping with its original digital atlas. We finally used the digital atlas of one of the baboons to study the individual kinetic of the main thalamus nuclei on Positron Emission Tomography (PET) images providing a novel and accurate way of measuring very fine and local functional differences.
ISSN:1959-0318
DOI:10.1016/j.irbm.2009.10.004