Telescience for Advanced Tomography Applications 1 Telescience featuring IPv6 enabled Telemicroscopy Steven Peltier National Center for Microscopy and.

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Presentation transcript:

Telescience for Advanced Tomography Applications 1 Telescience featuring IPv6 enabled Telemicroscopy Steven Peltier National Center for Microscopy and Imaging Research University of California, San Diego Steven Peltier National Center for Microscopy and Imaging Research University of California, San Diego Powered by the Internet2 Commons

Telescience for Advanced Tomography Applications 2 Description of the Telescience Project The International Collaboration Collaborative Process and Challenges

Telescience for Advanced Tomography Applications 3 Telemicroscopy Globus Enabled Computation Advanced Visualization Advanced Networking SRB Enabled Access to Distributed/Federated Databases Environment that Promotes Collaboration, Education and Outreach Partnership Remote Instrumentation Databases & Digital Libraries Computation Visualization Network Connectivity Collaboration, Education & Outreach Vision of Telescience

Telescience for Advanced Tomography Applications 4 3D Model of the Node of Ranvier IVEM Derive 3D information about a sample from a series of 2D projections Perfect application for driving the integration of technologies: Computation and data intensive Requires increased access to unique, expensive instrumentation Requires advanced visualization tools for segmentation and analysis of the data Detailed process well suited for collaboration Demand from neuroscience community for accelerated population of databases of biological structure Electron Tomography

Telescience for Advanced Tomography Applications 5 Application environment that provides centralized access to ALL tools/applications necessary for electron tomography with a Single Login from any Internet capable location Provides simple, intuitive access to sophisticated instrumentation and Grid resources for data storage and computation Provides a framework for future needs of high-throughput electron tomography The Telescience Portal

Telescience for Advanced Tomography Applications 6 Features of Telescience Portal Telemicroscopy via VidCon2 for remote instrumentation and data acquisition Parallel tomographic reconstruction using distributed, heterogeneous platforms and grid domains from a point-and-click interface Visualization, Segmentation, and Image processing tools Access to heterogeneous grid distributed systems for data management via The Storage Resource Broker (SRB) Transparent deposition of data products into Cell Centered Database (CCDB) Collaborative telecommunication utilities Shared “whiteboard" image annotations “Chatting” between multiple remote researchers

Telescience for Advanced Tomography Applications 7 Telescience Architecture Telescience Portal is composed of many “layers” Layers are modular, allowing for extension of each layer without disrupting the entire system Every Layer has its own complexity and administration that was previously passed on to the end-user Telescience Portal centralizes all administrative details of each layer into a single username and passphrase

Telescience for Advanced Tomography Applications 8 Grid Services

Telescience for Advanced Tomography Applications 9 Login Page

Telescience for Advanced Tomography Applications 10 Welcome Page

Telescience for Advanced Tomography Applications 11 Tomography Workflow Sequence of steps required to acquire, process, visualize, and extract useful information from a 3D volume. Problems with non-Portal “traditional” workflow: (~20) heterogeneous and platform specific tools: Simple shell scripts Parallel Grid enabled software Commercial software Administration is responsibility of the user Manual tracking, handling of data Advantages of workflow managed by Telescience Portal: Progress through the workflow can be organized and tracked Automated and transparent mechanisms for the flow of data Centralize tools and enhance operations with uniform GUIs to improve usability

Telescience for Advanced Tomography Applications 12 Telemicroscopy via VidCon2

Telescience for Advanced Tomography Applications 13 High Quality Digital Video over IPv6 Continuing research with collaborators in Osaka, Japan who are interested in latest technologies for sending high resolution digital video over next generation Internet protocols Remote access to 3 MeV microscope at Osaka University Advantages for Digital Video over IPv6: interactive video; 40Mbps and increasing, 30 fps quality of service improved security enhanced multicasting ability Tokyo XP (Chicago) STAR TAP TransPAC APAN vBNS (UC San Diego) SDSC NCMIR (San Diego) UHVEM (Osaka, Japan) JGN Osaka University

Telescience for Advanced Tomography Applications 14 Complete Abstraction of Grid No need to manage Globus Certificates Simply click resource(s) to use and enter biological parameters Resources are transparently cross-platform, cross-domain Globus Enabled Tomography (Gtomo)

Telescience for Advanced Tomography Applications 15 Image Processing JFido JViewer Pre-processing Utilities (ie. Fiducial marking, cropping, normalization) general 2D image viewer 3D contour visualization morphological measurements

Telescience for Advanced Tomography Applications 16 Advanced Visualization Technologies Synchronous client-server based visualization tool for volume rendering Center for Computational Visualization at the University of Texas ( Real-time interactive volume rendering with 2D transfer functions. Users can query data, define new opacity functions, and modify properties in real University of Utah Scientific Image and Computing Institute (

Telescience for Advanced Tomography Applications 17 SRB Collection Browser

Telescience for Advanced Tomography Applications 18

Telescience for Advanced Tomography Applications 19 Face to face meetings have been critical: –Organized around scientific meetings Biweekly H.323 (Polycom) meetings: – is used for daily communication, VTC meetings provide milestones in which to report progress –Further connect experts…place faces to messages Resource scientist working in Japan: carries domain expertise and is able to effectively translate as needed Collaborative Process and Lessons Learned

Telescience for Advanced Tomography Applications 20 Challenges General Challenges: Time differences often delay responses…limits ability to debug systems requiring interaction at both ends Language barrier: – seems to work well –diagrams and clear summaries w/ each meeting Technical Challenges: Network administration to configure the network end-to-end Software tuning for high bandwidth (DVTS) IPv6 deployment mismatch between countries

Telescience for Advanced Tomography Applications 21 Acknowledgements Telescience Participants: Telemicroscopy and Project Integration: National Center for Microscopy and Imaging Research Globus: Information Sciences Institute, University of Southern California GridPort: San Diego Supercomputer Center; Texas Advanced Computing Center Storage Resource Broker (SRB): San Diego Supercomputer Center Cell-Centered Database: University of California San Diego, Montana State University Interactive Collaboration Environments: Center for Computational Visualization, University of Texas Application-Level Scheduling (AppLeS) and Network Weather Service (NWS): University of California San Diego, University of California Santa Barbara International Collaborators: Advanced Networking and Computation: Cybermedia Center, Osaka University, Japan 3 MeV Microscopy: Center for UHVEM, Osaka University, Japan Visualization and Computation: National Center for High-Performance Computing (NCHC), Taiwan

Telescience for Advanced Tomography Applications 22