title: A 3D multi-modal and multi-dimensional digital brain model as a framework for data sharing.
abstract: Computer based three-dimensional reconstruction and co-registration of experimental data provide powerful tools for integration of observation derived from various technical approaches leading to better understanding of brain functions. Here we describe a method to build a 3D multi-modal and multi-dimensional model of brain structures providing framework for data sharing. All image processing, registration and 3D reconstruction were performed using open source software IMOD package software and ImageJ. The reconstruction procedure is based on series of AChE and Nissl stained sections aligned to blockface pictures. Integration of experimental data into the reference model is achieved by co-registration of Nissl sections of experimental brain cases by positioning landmarks on corresponding anatomical structures. To overcome the challenge of comparing for experimental sections with those of the reference model, adjustment of experimental model to the brain model was done section by section and limited to the structures of interest. For this adjustment we stress the use of cytoarchitectural criteria for accurate registration of anatomical structures and co-registration procedures.
authors.affiliation: Institut National de la Santé et de la Recherche Médicale UMRs 952, Centre National de Recherche Scientifique UMR 7224, Université Pierre et Marie Curie, 7-9 quai Saint Bernard, 75252, Paris Cedex 05, France. philippe.mailly@snv.jussieu.fr
authors.forename: Philippe
authors.initials: P
authors.lastname: Mailly
authors.forename: Suzanne N
authors.initials: SN
authors.lastname: Haber
authors.forename: Henk J
authors.initials: HJ
authors.lastname: Groenewegen
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Deniau
mesh_terms: D000110:Acetylcholinesterase / Q000737:chemistry / Q000378:metabolism; D000818:Animals; D001479:Basal Ganglia / Q000033:anatomy & histology; D001921:Brain / Q000033:anatomy & histology*; D002540:Cerebral Cortex / Q000033:anatomy & histology; D004396:Coloring Agents; D007091:Image Processing, Computer-Assisted; D007150:Immunohistochemistry; D048088:Informatics; D033181:Information Dissemination; D008297:Male; D008953:Models, Anatomic; D009434:Neural Pathways / Q000033:anatomy & histology; D051381:Rats; D017207:Rats, Sprague-Dawley; D012984:Software; D018998:Wheat Germ Agglutinin-Horseradish Peroxidase Conjugate
chemical_list: D004396:Coloring Agents; D018998:Wheat Germ Agglutinin-Horseradish Peroxidase Conjugate; D000110:Acetylcholinesterase