The merger of microscopy and advanced computing: A new frontier for the 21st century

Abstract

Establishing and maintaining state-of-the-art national resources such as HVEM, IVEM and supercomputing centers involves considerable initial cost and continued support of staff with special skills and knowledge. The increased availability of high performance computing and communications offers scientists the potential for effective remote interactive use of such centralized, specialized, and expensive facilities. Anticipating improvements in computing and communications infrastructure, a collaborative computational environment, or “Collaboratory for Microscopic Digital Anatomy” (CMDA), is being developed that will provide a researcher at a remote site distributed interaction with unique instrumentation for the acquisition and manipulation of biological images. The prototype outlined in figure 1 was developed at the San Diego Microscopy and Imaging Resource. The CDMA integrates remote interactive acquisition and analysis of 2- and 3-dimensional electron microscopic data from state-of-the-art digital image acquisition systems such as a computer-controled IVEM. A software system has been developed that provides interactive control of image acquisition from the IVEM from a remote laboratory (and eventually any laboratory on the Internet). Sophisticated software tools for image analysis, visualization, and data management of these digital images are also under development. The system design will provide transparent distribution of tasks that require extensive computation to high performance computers accessible on the network. These tasks include the derivation of 3-dimensional structure using electron microscope tomography, automatic feature extraction for serial section reconstructions as well as manipulation and exploration of 3-dimensional biological datasets.