Daniya Boges
ABSTRACT
We present a novel immersive environment for the interactive analysis of nanoscale cellular reconstructions of rodent brain samples acquired through electron microscopy. The system is focused on medial axis representations (skeletons) of branched and tubular structures of brain cells, and it is specifically designed for: i) effective semi-automatic creation of skeletons from surface-based representations of cells and structures ii) fast proofreading, i.e., correcting and editing of semi-automatically constructed skeleton representations, and iii) useful exploration, i.e., measuring, comparing, and analyzing geometric features related to cellular structures based on medial axis representations. The application runs in a standard PC-tethered virtual reality (VR) setup with a head mounted display (HMD), controllers, and tracking sensors. The system is currently used by neuroscientists for performing morphology studies on sparse reconstructions of glial cells and neurons extracted from a sample of the somatosensory cortex of a juvenile rat.
- Marco Agus, Daniya Boges, Nicolas Gagnon, Pierre J Magistretti, Markus Hadwiger, and Corrado Cali. 2018. GLAM: glycogen-derived Lactate Absorption Map for visual analysis of dense and sparse surface reconstructions of rodent brain structures on desktop systems and virtual environments. Computers & Graphics 74(2018), 85–98.Google Scholar
Cross Ref
- Corrado Calì, Jumana Baghabra, Daniya J. Boges, Glendon R. Holst, Anna Kreshuk, Fred A. Hamprecht, Madhusudhanan Srinivasan, Heikki Lehväslaiho, and Pierre J. Magistretti. 2016. Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues: 3D Virtual reality for neural tissue. Journal of Comparative Neurology 524, 1 (Jan. 2016), 23–38. https://doi.org/10.1002/cne.23852Google ScholarCross Ref
- Corrado Calì, Marco Agus, Kalpana Kare, Daniya Boges, Heikki Lehvaslaiho, Markus Hadwiger, and Pierre Magistretti. 2019. 3D cellular reconstruction of cortical glia and parenchymal morphometric analysis from Serial Block-Face Electron Microscopy of juvenile rat. Progress in Neurobiology (09 2019), 101696. https://doi.org/10.1016/j.pneurobio.2019.101696Google Scholar
- Lida Kanari, Paweł Dłotko, Martina Scolamiero, Ran Levi, Julian Shillcock, Kathryn Hess, and Henry Markram. 2018. A Topological Representation of Branching Neuronal Morphologies. Neuroinformatics 16, 1 (01 Jan 2018), 3–13. https://doi.org/10.1007/s12021-017-9341-1Google Scholar
- Lida Kanari, Srikanth Ramaswamy, Ying Shi, Sebastien Morand, Julie Meystre, Rodrigo Perin, Marwan Abdellah, Yun Wang, Kathryn Hess, and Henry Markram. 2019. Objective Morphological Classification of Neocortical Pyramidal Cells. Cerebral Cortex 29, 4 (01 2019), 1719–1735. https://doi.org/10.1093/cercor/bhy339 arXiv:http://oup.prod.sis.lan/cercor/article-pdf/29/4/1719/28075646/bhy339.pdfGoogle Scholar
- Mie Sato, Ingmar Bitter, Michael A. Bender, Arie E. Kaufman, and Masayuki Nakajima. 2000. TEASAR: Tree-Structure Extraction Algorithm for Accurate and Robust Skeletons. In Proceedings of the 8th Pacific Conference on Computer Graphics and Applications(PG ’00). IEEE Computer Society, Washington, DC, USA, 281–. http://dl.acm.org/citation.cfm?id=826029.826514Google ScholarCross Ref
- Ronell Sicat, Jiabao Li, JunYoung Choi, Maxime Cordeil, Won-Ki Jeong, Benjamin Bach, and Hanspeter Pfister. 2018. Dxr: A toolkit for building immersive data visualizations. IEEE transactions on visualization and computer graphics 25, 1(2018), 715–725.Google ScholarDigital Library
- Andrea Tagliasacchi, Ibraheem Alhashim, Matt Olson, and Hao Zhang. 2012. Mean Curvature Skeletons. Comput. Graph. Forum 31, 5 (Aug. 2012), 1735–1744. https://doi.org/10.1111/j.1467-8659.2012.03178.xGoogle ScholarDigital Library
- Will Usher, Pavol Klacansky, Frederick Federer, Peer-Timo Bremer, Aaron Knoll, Jeff Yarch, Alessandra Angelucci, and Valerio Pascucci. 2017. A virtual reality visualization tool for neuron tracing. IEEE transactions on visualization and computer graphics 24, 1(2017), 994–1003.Google Scholar
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