Submitted by:
Stephanie Sides
Manager, Documentation Services
User Services
San Diego Supercomputer Center
PO Box 85608
San Diego, CA 92186-9784 USA
v: (619) 534-5131
f: (619) 534-5117
e: sides@sdsc.edu
Categories:
Research, academic
Keywords:
Innovative or improved ways of doing things; More equitable access to technology or electronic information; Creation of new ideas, products, or services; Technology transfer; Local commitment to network-based activities; Leverage of public funding
Supporting Documentation (contact author for more information):
Video; Software; Documentation; Slides/photographs; Audio recordings
The Story:
Distributing the laboratory across the network
High-speed computer networks are enhancing the value of scientific investigations that are based on analyzing information from laboratory instrumentation. Such networks make feasible a system in which a laboratory scientist, working at a desktop workstation, can perform an investigation by deploying tasks to specialized scientific instruments and high-performance computers located at sites remote from the scientist.
One such project is the Microscopist’s Workstation. This project explores the concept of a “distributed laboratory” in which a researcher can acquire and process images of a biological specimen using a special electron microscope and high-performance computers in other locations.
This project is designed around the JEOL 4000EX intermediate high- voltage electron microscope (IVEM) located at the San Diego Microscopy and Imaging Resource (SDMIR). This project extends the capability of the microscope for scientific investigation by combining the traditional data acquisition process with computing power to render, view, and animate the images. The resulting synergy between a sophisticated scientific instrument and such interactive visualization techniques produces a more powerful investigative tool. In addition, this project makes the microscope usable by scientists in distant locations, thereby extending the sway of the resource and broadening the community that can use it.
By comparison with more commonly available lower-voltage microscopes, the IVEM can image considerably thicker biological specimens with greater contrast. Such images provide important information about the three-dimensional structure of the specimen. The microscope is being used to study the disruption of nerve cell components thought to be linked to Alzheimer’s disease, the structure of protein molecules involved in the release of calcium inside neurons, and the three-dimensional form of the Golgi apparatus, where sugars are added to proteins. The goal is relating biological structure with function.
To start an investigation, the specimen is loaded onto the microscope stage, and a low-resolution “survey” image is collected in digital form and transmitted to the remote researcher’s workstation. This workstation allows the investigator to roam across the survey image and request more highly magnified images, an image montage, or a stereo three-dimensional image for viewing. In addition, the investigator can collect a tomographic series of images (similar to CAT scan images). This series, in turn, can be sent via the network to a supercomputer, such as the CRAY Y-MP at the San Diego Supercomputer Center (SDSC), for automatic processing into a digital volume representing the interior of the specimen.
In the future, researchers working on this project plan to implement computer assisted focusing and calibration of the microscope (now handled by a human operator) and enhanced image-analysis tools. In addition, high-performance computing resources, including SDSC’s and other national centers’ parallel supercomputers, will be further integrated into this environment.
The Microscopist’s Workstation project is providing important information on how biological scientists interact with the microscope and their remote image acquisition and analysis requirements. This information will be used to improve local and remote graphics interfaces as well as network data-transfer subsystems. The system will be available for UNIX-based computers and the Apple Macintosh.
The Microscopist’s Workstation project is a collaborative effort among the SDMIR at the University of California, San Diego (UCSD) Medical School Department of Neurosciences, SDSC, the UCSD Department of Computer Science and Engineering, and The Scripps Research Institute (TSRI). The principal researchers include Mark H. Ellisman and Stephen J. Young (SDMIR); Philip J. Mercurio and T. Todd Elvins (SDSC); Kevin R. Fall (UCSD); and Philip S. Cohen (TSRI). Costs have been shared by the National Institutes of Health and the National Science Foundation, the State of and University of California, Sun Microsystems Computer Corporation, Datacube, Inc., Network Systems Corporation, and Photometrics Ltd.
(Just as a reminder, this story has also been submitted to Steve Griffin, NSF, for use in an all-federal-agency publication on HPCC, as agreed to by both NSFNET and FARNET previously.)