Database application for management of microscopic images

Abstract

Event Abstract Back to Event Database application for management of microscopic images J. O. Kjode1*, D. Darine1, T. B. Leergaard1 and J. G. Bjaalie1 1 University of Oslo, Norway Common to many neuroscience projects is that they generate vast numbers of images of histological sections from the brain. The sections have been processed with a variety of techniques, revealing information at the level of molecules, subcellular parts, cells, populations of cells, and overall regional organization in the brain. Efficient use of large collections of images, however, requires management of the data, providing convenient access to the data for multiple users, and analytical environments for systematic characterization and comparison of features observed in the images. We have developed a highly structured relational database system for archiving, retrieving, viewing, and analysing microscopic images captured from histological sections. The system is tailored for managing large amount of images, facilitating sharing and analysis of the data. The input to the system is 1) mosaic images acquired with microscopes equipped with high precision motorized stages and digital cameras, or images acquired with section scanners, 2) metadata describing the material and the experimental procedures, organized relative to experimental animal, tissue block, and histological sections. In addition, reference atlases must be entered into the system. Images of serial sections are stepwise co-registered to reference atlas diagrams by first anchoring each image to the nearest corresponding atlas diagram with use of anatomical landmarks, and secondly, by positioning and scaling a stereotaxic coordinate grid to the image. Database queries include search parameters for project name, species, procedures, structure names, and stereotaxic coordinates. Any of the parameters can be combined. Results are shown as a sorted list of experimental animals containing one or more hits (presented as an overview), with detailed information available for the animal, the tissue blocks, and the sections. Section images and experimental procedures can be downloaded. The system includes a virtual microscopy tool for viewing of series of section images, registered to the atlas diagrams. Thumbnails provide an overview of the images. The use of the Zoomify technology allows high resolution (multi-gigabyte) section images to be viewed, zoomed, and panned in a standard web-browser. Up to nine section images can be compared at once. The system also includes a tool containing 3-D atlas reconstructions (Hjornevik et al., Front. Neuroinform. 1:4. doi:10.3389/neuro.11.004.2007) allowing section images to be compared to a 3-D atlas framework. The 3-D framework can be sliced at any angle of orientation, making it possible to create atlas diagrams at non-standard angles. The system, referred to as Rodent Brain Navigator, is based on the J2EE Sun Microsystems standard and runs on Oracle application and database servers. The development is taking place with support of and coordinated by the INCF National Node of Norway. Supported by The Research Council of Norway. Conference: Neuroinformatics 2008, Stockholm, Sweden, 7 Sep - 9 Sep, 2008. Presentation Type: Poster Presentation Topic: Digital Atlasing Citation: Kjode J, Darine D, Leergaard T and Bjaalie J (2008). Database application for management of microscopic images. Front. Neuroinform. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.056 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: 28 Jul 2008; Published Online: 28 Jul 2008. * Correspondence: J. O. Kjode, University of Oslo, Oslo, Norway, janokj@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 J. O. Kjode D. Darine T. B. Leergaard J. G. Bjaalie Google J. O. Kjode D. Darine T. B. Leergaard J. G. Bjaalie Google Scholar J. O. Kjode D. Darine T. B. Leergaard J. G. Bjaalie PubMed J. O. Kjode D. Darine T. B. Leergaard J. 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.