Neurological diseases such as Parkison's and Alzheimer's are associated with the breakdown of components of the nervous system. The cellular and molecular basis for this degeneration has been extremely difficult to visualise in the past. A high-resolution 400.000 volt electron microscope is able to obtain images from much thicker specimens than conventional instruments can, thus allowing examination of 3-D biological structure and discovery of cellular changes that may result in disease. To promote remote access to such scarcely found high powered microscopes like the one residing at the San Diego National Centre for Microscopy and Imaging Research (NCMIR), a plan has been developed to build a "Collaboratory for Microscopy and Digital Anatomy" (CMDA), using Internet and high performance computing to support biomedical researchers.
In 1992, NCMIR and the San Diego Supercomputer Centre (SDSC) launched a project known as telemicroscopy to pioneer remote access to NCMIR's 400.000 volt microscope. Since the demonstration was successful, CMDA started out in 1994 as a five-year program to execute collaborative study in many critical areas in biomedical science, besides Parkinson's and Alzheimer's. NCMIR takes care of biological and instrumentation expertise while the National Partnership for Advanced Computational Infrastructure (NPACI) provides resources and expertise in system design, high performance computing and networking through the SDSC. The Program of Computer Graphics at Cornell University is responsible for the interactive visualisation tools.
At present, CMDA organises regular sessions with selected researchers who control the microscope and acquire images using a workstation. In the future, biologists will use a web browser by means of a Java application offering video feed of the microscope, which will largely improve the interactive control. The obtained images are singular 2-D series or images that can be used to reconstruct a 3-D view of the sample. The microscope stage being a mechanical device, small motions can cause slight shifts in the position of the specimen. Therefore, after comparison against the coordinates of its predecessor, the projected image is repositioned automatically by electronic means. The resulting aligned image set is called a "tilt series".
Next, the tilt series is run through a parallel tomography program reconstructing a 3-D view of the sample. The output, given in voxels aligned on a 3-D grid, is submitted to a direct volume rendering program on a SGI workstation where fine shading achieves the 3-D rendered image, ready to be used and manipulated by the researcher in his own laboratory. Through the CMDA remote interface, GridManager, the biologist is able to request few or high detailed images and control the specimen's position and magnification level from a distance. Rapid transfer of data between the remote user, the microscope and resources at SDSC is guaranteed via the very-high-speed Backbone Network Service (vBNS) of the National Science Foundation.
On top of this, CMDA researchers have created a general-purpose Asynchronous Communication Environment (ACE) to facilitate the transparent distribution of data and messages across the network among the remote users' workstations, the microscope control system and high performance computers. In the future, any system combining mechanical control of an instrument which doesn't necessarily have to be a microscope, compute-intensive operations, remote users and large data sets can benefit from this technology. CMDA has already proven to pay at least some contribution to the advancement in treatment of serious diseases such as Parkinson's and Alzheimer's. Please check in at the NCMIR site for more information on the CMDA program.