Portion of a nerve synaptic membrane. Image data were collected using electron tomography at UT Southwestern Medical Center and visualized using TACC resources.
Image Courtesy UT Southwestern Medical Center and TACC
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A collaboration of Texas researchers has opened a new window onto the world of cell biology. For the last six months, biologists from The University of Texas Southwestern Medical Center at Dallas have worked with computer scientists from the Texas Advanced Computing Center in Austin to produce a real-time, interactive remote visualization of cell structures.
The remote visualization has been used by UT Southwestern scientist Christopher Gilpin to investigate nerve synaptic membranes. The three-dimensional images were collected with an electron microscope at UT Southwestern, processed into a three-dimensional reconstruction and visualized at TACC. For the first time, Gilpin is able to interactively visualize and investigate a reconstruction of a synaptic membrane in real time from his desktop in Dallas.
"The images that we have produced are completely new, and we now have the enviable task of interpreting what we've seen," says Gilpin. "In the future we plan to do some genetic manipulation, changing the protein composition of the synaptic membrane and looking at how that affects structure."
The project takes advantage of imaging expertise at UT Southwestern, which has recently purchased new instrumentation for light and electron microscopy, and computing expertise at TACC. Gilpin collects imaging data and transfers it to TACC's Maverick system, where the visualization is processed. The pixels that make up the three-dimensional images are then transferred to Gilpin's desktop using VNC, the Virtual Network Computer protocol.
"VNC was developed a long time ago to do desktop sharing, and we have leveraged this technology for remote visualization," explains Kelly Gaither, a TACC researcher who has worked closely with Gilpin on the project. "VNC is very good at high-latency, low-bandwidth connections, which allows us to bring remote visualization to the common desktop. Chris needs to do interactive visualizations, and latency can be a big problem—if he moves his mouse, the image had better respond right away."
There is still work ahead for both sides of the collaboration. Gilpin will begin analyzing the nerve synaptic membranes, and plans to investigate more complex structures, starting with individual cell organelles. His goal is to visualize a complete cell, a task that will involve reconstructing and viewing 400-500 terabytes of data. To easily transfer so much data, Gaither hopes to incorporate grid tools such as GridFTP into the visualization process.
"Chris currently has to ship his data to TACC, which can take several days," she explains. "The grid tools are more sophisticated, but we still need to get higher-speed networks connecting his instruments and TACC."
Learn more at the UT Southwestern Medical Center and Texas Advanced Computing Center Web sites.
—Katie Yurkewicz
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