title: Three-dimensional reconstruction of stained histological slices and 3D non-linear registration with in-vivo MRI for whole baboon brain.
abstract: The correlation between post-mortem data and in-vivo brain images is of high interest for studying neurodegenerative diseases. This paper describes a protocol that matches a series of stained histological slices of a baboon brain with an anatomical MRI scan of the same subject using an intermediate 3D-consistent volume of "blockface" photographs taken during the sectioning process. Each stained histological section of the baboon brain was first registered to its corresponding blockface photograph using a novel "hemi-rigid" transformation. This piecewise rigid 2D transformation was specifically adapted to the registration of slices which contained both hemispheres. Subsenquently, to correct the global 3D deformations of the brain caused by histological preparation and fixation, a 3D elastic transformation was estimated between the blockface volume and the MRI data. This 3D elastic transformation was then applied to the histological volume previously aligned using the hemi-rigid method to complete the registration of the series of stained histological slices with the MRI data. We assessed the efficacy of our method by evaluating the quality of matching of anatomical features as well as the difference of volume measurements between the MRI and the histological images. Two complete baboon brains (with the exception of cerebellum) were successfully processed using our protocol.
authors.affiliation: Service Hospitalier Frédéric Joliot, CEA, Orsay, France. dauguet@crl.med.harvard.edu
authors.forename: Julien
authors.initials: J
authors.lastname: Dauguet
authors.forename: Thierry
authors.initials: T
authors.lastname: Delzescaux
authors.forename: Françoise
authors.initials: F
authors.lastname: Condé
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Mangin
authors.forename: Nicholas
authors.initials: N
authors.lastname: Ayache
authors.forename: Philippe
authors.initials: P
authors.lastname: Hantraye
authors.forename: Vincent
authors.initials: V
authors.lastname: Frouin
mesh_terms: D000818:Animals; D001921:Brain / Q000033:anatomy & histology*; D001931:Brain Mapping / Q000295:instrumentation / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000295:instrumentation / Q000379:methods; D008279:Magnetic Resonance Imaging / Q000379:methods*; D009445:Neuroanatomy / Q000295:instrumentation / Q000379:methods*; D009482:Neurophysiology / Q000295:instrumentation / Q000379:methods; D048531:Papio papio / Q000033:anatomy & histology*; D011180:Postmortem Changes; D013194:Staining and Labeling