title: Brain spatial normalization.
abstract: Neuroanatomical informatics, a subspecialty of neuroinformatics, focuses on technological solutions to neuroimage database access. Its current main goal is an image-based query system that is able to retrieve imagery based on anatomical location. Here, we describe a set of tools that collectively form such a solution for sectional material and that are available to investigators to use on their own data sets. The system accepts slide images as input and yields a matrix of transformation parameters that map each point on the input image to a standardized 3D brain atlas. In essence, this spatial normalization makes the atlas a spatial indexer from which queries can be issued simply by specifying a location on the reference atlas. Our objective here is to familiarize potential users of the system with the steps required of them as well as steps that take place behind the scene. We detail the capabilities and the limitations of the current implementation and briefly describe the enhancements planned for the near future.
authors: Laboratory for Bioimaging and Anatomical Informatics, Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA.
authors: William
authors: W
authors: Bug
authors: Carl
authors: C
authors: Gustafson
authors: Allon
authors: A
authors: Shahar
authors: Smadar
authors: S
authors: Gefen
authors: Yingli
authors: Y
authors: Fan
authors: Louise
authors: L
authors: Bertrand
authors: Jonathan
authors: J
authors: Nissanov
mesh_terms: D000818:Animals; D001921:Brain / Q000033:anatomy & histology*; D001931:Brain Mapping; D003628:Database Management Systems; D003952:Diagnostic Imaging; D007090:Image Interpretation, Computer-Assisted; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D012984:Software