Event Abstract Back to Event Automated Atlas Annotation for Transgenic Mouse Lines Ken Sugino1*, Yao Cheng1 and Sacha Nelson1 1 Brandeis University, United States The brain consists of a multitude of cell types that are connected in specific and intricate ways. The elucidation of neuronal cell types and their patterns of connection are critical steps in understanding brain function. However, while cellular phenotypes like morphology, marker expression and electrophysiology have successfully delineated component cell types in some brain regions, the identification of neuronal cell types in many other regions remains a matter of ongoing debate. Recently, transgenic mouse lines that label specific subpopulation of cells are being recognized as useful tools for the identification and investigation of neuronal cell types. Efforts in generating mouse lines for this purpose are underway in various places and a central database serving as a repository of information gained from those mouse lines is already established (http://www.credrivermice.org). Two of the most useful types of information needed for each cell type identified in a transgenic mouse lines are 1) the anatomical location of the labeled cells , and 2) the expression of previously recognized molecular markers, typically assessed in terms of the degree of overlap between cellular labeling and immunolabeling staining experiments. Those data can be analyzed manually, however, the work required is rather extensive (e.g.20 sections/line x 100 lines x 2 hr/section*person ~ 2 person-years) Hence, automated systems to replace or assist manual analysis are desired. Our approach for automated assignment of anatomical region consists of three steps: (1) detection of labeled cell bodies in each section, (2) registration of a series of sections from a given mouse line into a standard brain space such as Waxholm space, and (3) mapping the counts of detected cell bodies into anatomical regions assigned in the standard space. For the second problem of marker overlap counting, the cell body detection in one channel (i.e. step 1), is followed by detecting signal from one or more other channel (step 4). We have currently implemented steps (1) and (4), and are collaborating with other groups for realizing steps (2 and 3). Figure 1 Keywords: digital atlasing Conference: 4th INCF Congress of Neuroinformatics, Boston, United States, 4 Sep - 6 Sep, 2011. Presentation Type: Poster Presentation Topic: Digital atlasing Citation: Sugino K, Cheng Y and Nelson S (2011). Automated Atlas Annotation for Transgenic Mouse Lines. Front. Neuroinform. Conference Abstract: 4th INCF Congress of Neuroinformatics. doi: 10.3389/conf.fninf.2011.08.00035 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. Ken Sugino, Brandeis University, Waltham, United States, sugino@brandeis.edu 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 Ken Sugino Yao Cheng Sacha Nelson Google Ken Sugino Yao Cheng Sacha Nelson Google Scholar Ken Sugino Yao Cheng Sacha Nelson PubMed Ken Sugino Yao Cheng Sacha Nelson 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.