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L'IMAGERIE POST MORTEM TRIDIMENSIONNELLE CEREBRALE : CONSTITUTION ET APPORT POUR L'ANALYSE CONJOINTE DE DONNEES HISTOLOGIQUES ANATOMO-FONCTIONNELLES ET LA MISE EN CORRESPONDANCE AVEC L'IMAGERIE IN VIVO.

Abstract : The 3D reconstruction of histological slices yields a new modality that we call Post Mortem Imaging (PMI). In this thesis, we propose a classification for brain histology studies, and we describe two protocols for the constitution of cerebral PMI. The first protocol deals with animals such as rodents. It includes the acquisition and the extraction of anatomical (stained histological slices) and functional (autoradiographies) series. This step is followed by the alignment and the coalignment of the histological slices to constitute anatomical and functional volumes that are spatially consistent and registered, allowing the performance of 3D analysis. The second protocol deals with animals such as primates. It describes a complete method for matching in vivo and post mortem data. A volume of histological slices is obtained by coalignement with block face photographs taken of the brain during the cutting process. Furthermore, a robust inter-slice intensity normalisation is proposed to recover intensity 3D consistency. Finally, an elastic deformation is estimated between the post mortem brain and the brain in its in vivo geometry (embodied by the MRI data) to correct for volume differences related to histology. As direct applications of this protocol, we present the creation of atlases of the thalamus, which are compared to an in vivo segmentation of the thalamus realized on diffusion MRI data using a new method based on classification mechanisms. We conclude this work through the utilisation of PMI and its prospects for the future.
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https://tel.archives-ouvertes.fr/tel-00339418
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Submitted on : Monday, November 17, 2008 - 6:53:55 PM
Last modification on : Friday, October 23, 2020 - 4:33:48 PM
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Julien C. Dauguet. L'IMAGERIE POST MORTEM TRIDIMENSIONNELLE CEREBRALE : CONSTITUTION ET APPORT POUR L'ANALYSE CONJOINTE DE DONNEES HISTOLOGIQUES ANATOMO-FONCTIONNELLES ET LA MISE EN CORRESPONDANCE AVEC L'IMAGERIE IN VIVO.. Interface homme-machine [cs.HC]. Ecole Centrale Paris, 2005. Français. ⟨tel-00339418⟩

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