Event Abstract Back to Event Rodent Brain Navigator: database and atlas system for microscopy and imaging data Ivar Moene1*, Dmitri Darine1, Muthuraja Ramachandran1, Trygve B. Leergaard1 and Jan G Bjaalie1 1 University of Oslo, Norway Rodent Brain Navigator is a highly structured relational database system for archiving, retrieving, viewing, and analyzing multiple categories of microscopy and imaging data in standardized brain atlas space. The application is running on an Apache Tomcat server and an Oracle database. The present version is prepared for serial section data, typically consisting of high-resolution mosaic images covering complete histological sections through the rat and mouse brain. A modified version of the system is being prepared for management of volumetric data, collected with microscopic MRI or small animal PET. Modules for registration of serial section images and volume data to standardized mouse and rat brain atlases are being developed. Registration procedures are intended to be semi-automatic, using landmarks, architectonic boundaries and pattern recognition as reference information. Metadata, describing the experimental animal, the extracted tissue blocks, the histological sections, and the microscopy data acquisition procedures, are uploaded together with the primary section image data. Queries are based either on the metadata (e.g., presence of molecules or markers) or on spatial coordinates. Queries for structure names (based on registration to atlases) will be available in future versions. Search entries may be combined and reiterated. Results are shown as lists of section images sorted by experimental animal. The user then selects all, or subsets of the section images that were retrieved, for display in 2-D viewers. The viewers facilitate comparisons of multiple images and image combinations, and allow inspection of images coupled to the atlas framework. Overall, the system is tailored for management of large amounts of section image data collected in the context of research projects within a laboratory or a consortium of laboratories. Rat Brain Navigator developments are supported by The Research Council of Norway. The project is one of several coupled to the INCF Norwegian National Node, hosted by the Centre for Molecular Biology and Neuroscience, University of Oslo. Keywords: digital atlasing, Neuroimaging Conference: 4th INCF Congress of Neuroinformatics, Boston, United States, 4 Sep - 6 Sep, 2011. Presentation Type: Poster Presentation Topic: Digital atlasing Citation: Moene I, Darine D, Ramachandran M, Leergaard T and Bjaalie J (2011). Rodent Brain Navigator: database and atlas system for microscopy and imaging data. Front. Neuroinform. Conference Abstract: 4th INCF Congress of Neuroinformatics. doi: 10.3389/conf.fninf.2011.08.00159 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 17 Oct 2011; Published Online: 19 Oct 2011. * Correspondence: Dr. Ivar Moene, University of Oslo, Oslo, Norway, i.a.moene@medisin.uio.no Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Ivar Moene Dmitri Darine Muthuraja Ramachandran Trygve B. Leergaard Jan G Bjaalie Google Ivar Moene Dmitri Darine Muthuraja Ramachandran Trygve B. Leergaard Jan G Bjaalie Google Scholar Ivar Moene Dmitri Darine Muthuraja Ramachandran Trygve B. Leergaard Jan G Bjaalie PubMed Ivar Moene Dmitri Darine Muthuraja Ramachandran Trygve B. Leergaard Jan G Bjaalie Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.