Workflow for integration and analysis of histological data in rodent brain Waxholm Space

Event Abstract Back to Event Workflow for integration and analysis of histological data in rodent brain Waxholm Space Eszter A. Papp1, Trygve B. Leergaard1, Gergely Csucs1, Dmitri A. Darine1 and Jan G. Bjaalie1* 1 University of Oslo, Institute of Basic Medical Sciences, Norway Identification and analysis of distribution of various cellular markers visualized in histological materials are fundamental to many experimental investigations in the rodent brain. Since investigations of distributed brain systems and manifestations of ageing and brain disease across the brain often require brain-wide analysis, technologies for efficient acquisition of large amounts of image data from individual brains are increasingly used. A major challenge in this context is the task of analyzing large amounts of high-resolution image data and identifying the anatomical regions and subregions in which the labelled cellular elements are observed. To this end, common reference frameworks are introduced, including brain atlases with standardized brain atlas space, such as the recently introduced volumetric Waxholm Space atlases developed for the mouse and rat brain (Hawrylycz et al., 2011; Papp et al., 2014). We here present a workflow aimed at providing 1) automatic, or semi-automatic identification of labeling in large series of microscopic section images acquired with robotic microscopes or slide scanners, 2) spatial anchoring of histological section images to the volumetric Waxholm Space atlases, and 3) atlas based analysis of the distribution of labelling. The work flow begins with histological section image data and ends with the analysis of data anchored to the Waxholm Space atlases. Automated analyses include image filtering to identify and quantify labelling, and assignment of spatial location parameters to determine where in the brain labelling is located. The workflow was tested using experimental material from recently published studies on brain-wide mapping of axonal connections in the rat and distribution of genetic markers in transgenic mouse models of neurodegenerative disease. High-resolution images of complete coronal, sagittal or horizontal sections were acquired using a slidescanning system. Image processing parameters were optimized on selected representative sections, and then applied to complete image series. Within a wide range of labeling densities, the automatic method provided reliable results and offered opportunities for efficient, standardized analysis of labeling distribution across the brain. The work flow presented, with the concepts and tools provided, allows efficient registration of section image data to a volumetric reference atlas and brain-wide analysis of histologically labelled cellular markers. Acknowledgements Supported by grants from the Research Council of Norway and the EC Human Brain Project to J.G.B. References Hawrylycz M, Baldock RA, Burger A, Hashikawa T, Johnson GA, Martone M, Ng L, Lau C, Larson SD, Nissanov J, Puelles L, Ruffins S, Verbeek F, Zaslavsky I, Boline J (2011). Digital atlasing and standardization in the mouse brain. PLoS Comput Biol 7, e1001065 Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014). Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage, in press. doi: 10.1016/j.neuroimage.2014.04.001 Keywords: digital brain atlas, Histology, image analysis, Mouse brain template, neuroinformatics, Rat brain template, Spatial registration, Waxholm Space, workflow Conference: Neuroinformatics 2014, Leiden, Netherlands, 25 Aug - 27 Aug, 2014. Presentation Type: Poster, not to be considered for oral presentation Topic: Digital atlasing Citation: Papp EA, Leergaard TB, Csucs G, Darine DA and Bjaalie JG (2014). Workflow for integration and analysis of histological data in rodent brain Waxholm Space. Front. Neuroinform. Conference Abstract: Neuroinformatics 2014. doi: 10.3389/conf.fninf.2014.18.00060 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: 27 Apr 2014; Published Online: 04 Jun 2014. * Correspondence: Prof. Jan G Bjaalie, University of Oslo, Institute of Basic Medical Sciences, Oslo, N-0317, Norway, j.g.bjaalie@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 Eszter A Papp Trygve B Leergaard Gergely Csucs Dmitri A Darine Jan G Bjaalie Google Eszter A Papp Trygve B Leergaard Gergely Csucs Dmitri A Darine Jan G Bjaalie Google Scholar Eszter A Papp Trygve B Leergaard Gergely Csucs Dmitri A Darine Jan G Bjaalie PubMed Eszter A Papp Trygve B Leergaard Gergely Csucs Dmitri A Darine 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.