Tele-microscopy project applies grid technologies to study the brain
San Diego 09 November 2001The smallest components of nerve cells can reveal fundamental insights into how the brain and nervous system work. To study these tiny structures in their natural environment requires access to extremely scarce advanced imaging instruments and powerful computer resources. The Telescience alpha project is harnessing the power of information grids to enable neuroscientists to unravel the complex interactions of molecular and cellular biological structures which underlie thinking and learning and give rise to debilitating diseases of the brain, such as Parkinson's and Alzheimer's.
The Telescience alpha project is creating a set of tools to allow researchers to go seamlessly through the steps required to create images on a remote high energy microscope, use sophisticated software programmes to compute the 3D structures, called electron tomographic volumes, and deposit the most useful representations of these results into a database forming a library of computerised cell-level brain structures. As a result of this work, scientists and students in any location, using a reasonable network connection and a modern Web browser, will be able to harness these advanced capabilities.
The Telescience alpha projects consist of seven application-driven initiatives, launched by the United States National Partnership for Advanced Computational Infrastructure (NPACI) in order to provide greater cross-thrust interactions as multi-institutional teams collaborate to produce new software infrastructure for use by the national research community. This particular project on Telescience for Advanced Tomography Applications is developing and deploying infrastructure that provides Web-based access to distributed resources such as remote imaging instruments, remote heterogeneous parallel computers, federated and distributed databases, and image archives and component-based remote visualisation services.
The following applications and technologies are involved:
- Globus: Carl Kesselman, University of Southern California
- Application-Level Scheduling (AppLeS): Fran Berman, University of California San Diego (UCSD); Rich Wolski, University of Tennessee
- Network Weather Service (NWS): Rich Wolski, University of Tennessee
- Storage Resource Broker (SRB): Reagan Moore, San Diego Supercomputer Center (SDSC)
- Interactive Collaboration Environments: Chandrajit Bajaj, University of Texas
- Tele-microscopy: Mark Ellisman, UCSD
- Multi-scale Database: Mark Ellisman, UCSD; Gwen Jacobs, Montana State University
With a current focus on grid computing, the project has integrated tele-microscopy, an early parallel tomography code, and tools such as Globus, AppLeS, and NWS. Work continues in visualisation, computational methods for larger data sets, and distributed multi-scale databases, with integration of all these components in the course of 2001. The project is collaborating with the NPACI HotPage and the more generalised GridPort to develop Web-based solutions for computing, authentication, security, resource discovery, and data movement on the PACI Grid.
Globus tomography software has been in production use by scientists at the National Center for Microscopy and Imaging Research (NCMIR) throughout 2001, and researchers from laboratories in the United States and abroad now apply the tele-microscopy system on a regular basis. Successful Trans-Pacific tele-microscopy experiments have been carried out with the Osaka University Research Center for Ultra-High Voltage Electron Microscopy, and similar work has begun with researchers at the Karolinska Institute in Sweden.
The current NCMIR tele-microscopy system enables investigators at remote sites to interactively steer the 400.000-volt electron microscope at UCSD, acquire images of biological specimens, and perform most of the actions of an operator at the instrument's main console. The Telescience tool suite is applying grid technologies to link the microscope to distributed parallel computers for performing tomographic reconstruction, a technique which uses a set of image projections at different angles to derive 3D models of specimens.
Since conventional network transmission is too slow to offer image transmission rates sufficient for visually guided remote instrument control, the current design of the Collaboratory for Microscopic Digital Anatomy (CMDA) relies on a co-ordinated map of the specimen to guide the selection of specimen position, and automated functions. It is anticipated that network transmission rates will be considerably faster in the future. With higher transmission rates, visually guided interactive control of the microscope will become feasible. A new project called 6tele, developed in collaboration with groups at ESnet, Osaka University, the National Laboratory for Applied Network Research (NLANR), and Sun Microsystems, became one of the first scientific applications to run end-to-end over the next-generation IPv6 Internet protocol.
This year, automated data acquisition has been integrated with Globus tomography for live tomographic reconstruction and measurement of error and confidence levels. Automated archiving, search, and retrieval across multiple scales has been made possible with the multi-scale brain database. Analysis and measurement tools specialised for biological samples have enabled 3D visualisation. In the near future, co-scheduling of distributed tasks will be possible with efficient resource discovery including computing, memory, and networks as well as adaptive scheduling. Quantitative information from graphical models will enable computationally guided refinement of data acquisition.
The other Telescience alpha projects are focused around the development of:
More information is available at the NPACI Web site.
- a Bio-informatics infrastructure for large-scale analyses
- Protein folding in a distributed computing environment
- Multi-component models for energy and the environment
- a Scalable visualisation toolkit for bays to brains
- Adaptive computations for fluids in biological systems
- Monte Carlo cellular micro-physiology on the Grid
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