Registration of serial two-photon data to rodent brain Waxholm Space

Event Abstract Back to Event Registration of serial two-photon data to rodent brain Waxholm Space Trygve B. Leergaard1*, Christopher Coello1, Eszter A. Papp1, Tim Ragan2 and Jan G. Bjaalie1 1 University of Oslo, Institute of Basic Medical Sciences, Norway 2 TissueVision, Inc, United States Serial two-photon tomography (STPT) is a novel method combining vibratome sectioning with two-photon block-face imaging to produce volumetric representation of fluorescent markers at cellular resolution across entire organs, such as the mouse or rat brain (Ragan et al., 2012). Performing brain-wide analysis of the distribution of the visualized cellular objects and integration of large data sets across individual specimens require the use of efficient and automatized neuroinformatics pipelines. This work presents a procedure to register STPT data to the recently introduced Waxholm Space atlases developed for the mouse and rat brain (Hawrylycz et al., 2011; Papp et al., 2014). With the use of these digital atlas resources, available through the INCF Software Center, STPT data can be integrated in standardized 3-D space. The proposed pipeline takes as input series of high-resolution STPT images (0.82 µm2) capturing tissue (auto)fluorescence. These series of optical section images are spaced without gap at regular intervals (50 µm) across entire C57/Bl6 mouse or Sprague Dawley rat brains. Each slice is independently corrected for uneven illumination and contrast adjusted to optimize structural contrast of STPT data. Volumetric data are then generated by combining these slices and resampling the voxels to 25 µm3. A synthetic registration target volume, matching the signal intensity distributions of the STPT volume, was derived from the mouse and rat Waxholm Space templates. STPT volumes are warped to the synthetic target volume using a multi-step parametric registration procedure including rigid, affine and non-linear transformations. The spatial accuracy of the full procedure was evaluated by comparing a collection of selected anatomical reference structures, manually defined in the STPT volumes with corresponding landmarks defined in the mouse and rat Waxholm Space MRI templates. This procedure thus allows efficient registration of STPT autofluorescence images to mouse and rat Waxholm Space and represents one of several new digital atlasing approaches for anatomical analysis and data integration in rodent brain models. 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 Ragan T, Kadiri LR, Venkataraju KU, Bahlmann K, Sutin J, Taranda J, Arganda-Carreras I, Kim Y, Seung HS, Osten P (2012). Serial two-photon tomography for automated ex vivo mouse brain imaging. Nat Methods 9:255-258 Keywords: digital brain atlas, Mouse brain template, Neuroimaging, neuroinformatics, Rat brain template, Serial two-photon tomography, spatial normalization, Waxholm Space Conference: Neuroinformatics 2014, Leiden, Netherlands, 25 Aug - 27 Aug, 2014. Presentation Type: Poster, not to be considered for oral presentation Topic: Digital atlasing Citation: Leergaard TB, Coello C, Papp EA, Ragan T and Bjaalie JG (2014). Registration of serial two-photon data to rodent brain Waxholm Space. Front. Neuroinform. Conference Abstract: Neuroinformatics 2014. doi: 10.3389/conf.fninf.2014.18.00059 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: Dr. Trygve B Leergaard, University of Oslo, Institute of Basic Medical Sciences, Oslo, Norway, t.b.leergaard@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 Trygve B Leergaard Christopher Coello Eszter A Papp Tim Ragan Jan G Bjaalie Google Trygve B Leergaard Christopher Coello Eszter A Papp Tim Ragan Jan G Bjaalie Google Scholar Trygve B Leergaard Christopher Coello Eszter A Papp Tim Ragan Jan G Bjaalie PubMed Trygve B Leergaard Christopher Coello Eszter A Papp Tim Ragan 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.