Service.3dbar.org – online reconstruction of three-dimensional brain structures

Abstract

Event Abstract Back to Event service.3dbar.org – online reconstruction of three-dimensional brain structures Jakub M. Kowalski1*, Piotr Majka1 and Daniel K. Wójcik1 1 Nencki Instytute of Experimental Biology, Department of Neurophysiology, Poland The knowledge of brain anatomy has been one of the foundations of neuroscience since its beginning. Traditionally the reference for brain structures has been provided by printed brain atlases containing at least one series of planar parallel brain sections containing a map of the intersected structures. However, the brain structure is three-dimensional and it is much more convenient to use three-dimensional brain atlases if possible. In order to make precious anatomical information from two-dimensional atlases available in 3D, we have developed 3D Brain Atlas Reconstructor (3dBAR) software – a free, open source solution for performing automatic reconstruction of brain structure models from two-dimensional atlases. The 3dBAR consists of a reconstructor software, a set of tools to perform conversion of existing atlases to Common Atlas Format (CAF) and a Python module for reconstructing structures from CAF data. As 3dBAR is a complex offline package we provide some of its functionality as an online service. First, we provide a repository of free atlases (derived mainly from Scalable Brain Atlas – http://scalablebrainatlas.incf.org and Waxholm Space atlases) in CAF format, available to download and use with our software with no further conversion necessary. One can also download already reconstructed models of basic structures of different quality and format. It is also possible to request customized reconstructions (e.g. processed with non-standard pipeline or generating result in an additional file format) using on-line reconstruction wizard. The service facilities are available to the user via a browser based interface. We also provide an interface for communication with external services and third-party applications. The mechanism provided is so flexible that the user web interface can be realized as a javascript-based client application and so is compatible with most of modern web browsers. Currently, Scalable Brain Atlas contains a plugin using our service to visualize particular structures and download their reconstructions. The service functionality is also shared with WaxML services developed by the INCF DAI. Our plans include also combining the service facilities with neurosimulation software. Acknowledgements The project is supported from POIG.02.03.00-00-003/09 grant. Keywords: 3d Brain Atlas Reconstructor, 3d brain structures, 3dBAR, anatomical information, Online, reconstruction, repository, Service Conference: Bernstein Conference 2012, Munich, Germany, 12 Sep - 14 Sep, 2012. Presentation Type: Poster Topic: Data analysis, machine learning, neuroinformatics Citation: Kowalski JM, Majka P and Wójcik DK (2012). service.3dbar.org – online reconstruction of three-dimensional brain structures. Front. Comput. Neurosci. Conference Abstract: Bernstein Conference 2012. doi: 10.3389/conf.fncom.2012.55.00004 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: 07 May 2012; Published Online: 12 Sep 2012. * Correspondence: Mr. Jakub M Kowalski, Nencki Instytute of Experimental Biology, Department of Neurophysiology, Warsaw, województwo Mazowieckie, 02-093, Poland, j.kowalski@nencki.gov.pl 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 Jakub M Kowalski Piotr Majka Daniel K Wójcik Google Jakub M Kowalski Piotr Majka Daniel K Wójcik Google Scholar Jakub M Kowalski Piotr Majka Daniel K Wójcik PubMed Jakub M Kowalski Piotr Majka Daniel K Wójcik 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.