Event Abstract Back to Event Projectome: Set up and testing of a High Performance Computational Infrastructure for processing and visualizing neuro-anatomical information obtained using confocal ultra-microscopy techniques Ludovico Silvestri1*, Alessandro Bria2, Leonardo Sacconi1, Anna Letizia Allegra Mascaro1, Maria Chiara Pettenati3, Sanzio Bassini4, Carlo Cavazzoni4, Giovanni Erbacci4, Roberta Turra4, Giuseppe Fiameni4, Valeria Ruggiero5, Paolo Frasconi6, Simone Marinai6, Marco Gori7, Paolo Nesi6, Renato Corradetti8, Giulio Iannello2 and Francesco Saverio Pavone9 1 LENS, Italy 2 UCBM, Italy 3 ICON, Italy 4 CINECA, Italy 5 UNIFE, Italy 6 DSI - UNIFI, Italy 7 DiSI - UNISI, Italy 8 Neuroscience - UNIFI, Italy 9 ICON, LENS, Italy In Projectome we set up an IT infrastructure to share both neuroscience data as well as high performance computational applications. Data handled in Projectome are mouse brain images obtained using conf-u [1], a confocal ultra-microscopy technique in which selectively labeled neurons are imaged by light-sheet based microscopy [2][3] with micron-scale resolution. Data obtained from an experiment conducted on a mouse brain (1 cubic cm) might be of a range of 1 Terabyte, or more. Specific processes have been implemented in a Projectome Tooolkit in order to allow: 1) fully automated 3D Stitching capability starting from acquired raw data and 2) semi-automatic extraction of some morphological characteristics (eg. neurons localization) [1][4]. The implementation plan of the project consists of two phases: phase I, in which the core data management functions are set up and phase II in which the data mining, knowledge extraction and visualization features are implemented. Projectome is running the final part of phase I: both raw and processed data as well as elaboration algorithms are made available through a dedicated storage and computational infrastructure operated by CINECA, the largest Italian computing center [5]. Data sets originated from the European Laboratory of Non-linear Spectroscopy LENS [6] are transferred to CINECA using high performance protocol (i.e. GridFTP) and successively stored using iRODS data grid [7]. The setup of a Workflow Management System for the execution of Projectome Toolkit applications is being implemented using UNICORE [8]. [1] Silvestri, Bria, Sacconi, Iannello and Pavone, Confocal ultramicroscopy: micron-scale neuroanatomy of the entire mouse brain (2012). Submitted paper [2] Dodt et al., Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain, Nat Methods (2007) [3] Keller and Dodt, Light sheet microscopy of living or cleared specimens, Curr Opin Neurobiol (2011) – REVIEW [4] Bria, Silvestri, Sacconi, Pavone and Iannello, Stitching Terabyte-sized 3D images acquired in confocal ultramicrocopy, IEEE International Symposium on Biomedical Imaging (ISBI 2012), Barcelona, Spain, 2-5 May, 2012 [5] http://www.cineca.it/en [6] http://www.lens.unifi.it/ [7] iRODS (Integrated Rule-Oriented Data System) https://www.irods.org/ [8] UNICORE (Uniform Interface to Computing Resources) http://www.unicore.eu/ Keywords: Neuroimaging Conference: 5th INCF Congress of Neuroinformatics, Munich, Germany, 10 Sep - 12 Sep, 2012. Presentation Type: Poster Topic: Neuroinformatics Citation: Silvestri L, Bria A, Sacconi L, Allegra Mascaro A, Pettenati M, Bassini S, Cavazzoni C, Erbacci G, Turra R, Fiameni G, Ruggiero V, Frasconi P, Marinai S, Gori M, Nesi P, Corradetti R, Iannello G and Pavone F (2014). Projectome: Set up and testing of a High Performance Computational Infrastructure for processing and visualizing neuro-anatomical information obtained using confocal ultra-microscopy techniques. Front. Neuroinform. Conference Abstract: 5th INCF Congress of Neuroinformatics. doi: 10.3389/conf.fninf.2014.08.00129 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: 21 Mar 2013; Published Online: 27 Feb 2014. * Correspondence: Dr. Ludovico Silvestri, LENS, Sesto Fiorentino Firenze, Italy, silvestri@lens.unifi.it 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 Ludovico Silvestri Alessandro Bria Leonardo Sacconi Anna Letizia Allegra Mascaro Maria Chiara Pettenati Sanzio Bassini Carlo Cavazzoni Giovanni Erbacci Roberta Turra Giuseppe Fiameni Valeria Ruggiero Paolo Frasconi Simone Marinai Marco Gori Paolo Nesi Renato Corradetti Giulio Iannello Francesco Saverio Pavone Google Ludovico Silvestri Alessandro Bria Leonardo Sacconi Anna Letizia Allegra Mascaro Maria Chiara Pettenati Sanzio Bassini Carlo Cavazzoni Giovanni Erbacci Roberta Turra Giuseppe Fiameni Valeria Ruggiero Paolo Frasconi Simone Marinai Marco Gori Paolo Nesi Renato Corradetti Giulio Iannello Francesco Saverio Pavone Google Scholar Ludovico Silvestri Alessandro Bria Leonardo Sacconi Anna Letizia Allegra Mascaro Maria Chiara Pettenati Sanzio Bassini Carlo Cavazzoni Giovanni Erbacci Roberta Turra Giuseppe Fiameni Valeria Ruggiero Paolo Frasconi Simone Marinai Marco Gori Paolo Nesi Renato Corradetti Giulio Iannello Francesco Saverio Pavone PubMed Ludovico Silvestri Alessandro Bria Leonardo Sacconi Anna Letizia Allegra Mascaro Maria Chiara Pettenati Sanzio Bassini Carlo Cavazzoni Giovanni Erbacci Roberta Turra Giuseppe Fiameni Valeria Ruggiero Paolo Frasconi Simone Marinai Marco Gori Paolo Nesi Renato Corradetti Giulio Iannello Francesco Saverio Pavone 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.