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iSGTW Feature - Electron microscopy via the grid

Feature - Electron tomography without the headaches

Image courtesy of Belin Czechowicz, sxc.hu

Seeing is understanding

For biologists, seeing a structure's shape is the all-important step to understanding how it works. Just as in the architecture of a well-designed building, form follows function.

So, when a 17th century Dutch draper who enjoyed grinding lenses as a hobby invented the microscope, Anton van Leeuwenhoek revolutionized biology.

Microbiologists today may find their next tool coming from a source just as unlikely-academic computing.

By using the grid and a number of super-slim electron scans of an object taken at a variety of angles, researchers can create 3-D views up to 2 million times real size.

In spite of its usefulness for the field of microbiology, this process, known as electron tomography, has long remained unpractical for many researchers, as it is too computationally expensive.

But a project called EGEETomo, centered at University of Almería, in Spain, is building a tool to make this technology more accessible, says Roman Bilbao-Castro, EGEETomo developer.

Hepatitis B virus, as it appeared in the journal Ultramicroscopy.
Image courtesy of EGEETomo

The gift of grid

"Of course we can use supercomputers to perform such heavy reconstructions-with the consequent costs-but the grid gives us a new opportunity to put virtually unlimited computational resources in the hands of the 3-D electron microscopy researchers," he says.

While the nuts and bolts of the process remain complicated, the application is designed to be as automatic and user-friendly as possible: no sending of jobs, no replacing of experimental data, no need to learn new technological skills. Developers of EGEETomo are determined that their users will see the benefits of using a grid, with none of the headaches. A copy of the program's first working release is available from EGEETomo server for interested users.

"The work developed for EGEETomo is just the beginning for a new way of working in the field of 3-D electron microscopy. The long-term objective is to completely integrate 3-D EM with the computational resources present on the grid," says Bilbao-Castro.

"This presents two great challenges. We must develop our tool on the ever-evolving infrastructure of the grid, and we must reach a high quality product that encourages potential users to adopt a new working paradigm. We are conscious of the difficulty of successfully achieving both objectives but are also committed to making this a reality."

-Danielle Venton, iSGTW

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