Rodent Brain Navigator: database and atlas system for microscopy and imaging data

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.