title: A low temperature embedding and section registration strategy for 3D image reconstruction of the rat brain from autoradiographic sections.
abstract: In studies on animal models of human brain pathologies, three-dimensional reconstruction from histological sections is particularly useful when assessing the morphologic, functional and biochemical changes induced by pathology. It allows assessing lesion heterogeneity in planes different from the cutting plane and allows correlating the histology with images obtained in vivo, such as by means of magnetic resonance imaging. To create a 3D volume from autoradiographic sections with minimal distortion, both cryosectioning as well as section registration need to be optimal. This paper describes a strategy whereby four external fiducial markers are positioned outside the rat brain with the use of a low temperature brain embedding procedure. The fiducial markers proposed here can be rapidly added to any frozen tissue block with no impact on the subsequent histological operations. Since embedding is performed at a low temperature, no tissue degradation occurs due to sample heating. The markers enable robust and almost error free registration, even in the presence of missing sections and poor image quality. Furthermore, the markers may be used to partially correct for global distortions.
authors.affiliation: INSERM, Unité mixte 594, Neuroimagerie Fonctionnelle et Métabolique, Centre Hospitalier Universitaire Pavillon B, BP217, F-38043 Grenoble Cedex 09, France; Université Joseph Fourier, Grenoble F-38043 Cedex 09, France.
authors.forename: Arjan W
authors.initials: AW
authors.lastname: Simonetti
authors.forename: Vedat A
authors.initials: VA
authors.lastname: Elezi
authors.forename: Régine
authors.initials: R
authors.lastname: Farion
authors.forename: Grégoire
authors.initials: G
authors.lastname: Malandain
authors.forename: Christoph
authors.initials: C
authors.lastname: Segebarth
authors.forename: Chantal
authors.initials: C
authors.lastname: Rémy
authors.forename: Emmanuel L
authors.initials: EL
authors.lastname: Barbier
mesh_terms: D000178:Acrylamides; D000818:Animals; D001345:Autoradiography / Q000379:methods*; D001921:Brain / Q000033:anatomy & histology*; D002560:Cerebrovascular Circulation / Q000502:physiology; D016616:Cryoultramicrotomy; D003952:Diagnostic Imaging; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008297:Male; D051381:Rats; D017208:Rats, Wistar; D013696:Temperature; D016610:Tissue Embedding / Q000379:methods*
chemical_list: D000178:Acrylamides