Center for Integrative Biomedical Computing

Bridging the BioPSE Environment with the Telescience Grid

Steven Peltier, M.S./NCMIR

The National Center for Microscopy and Imaging Research (NCMIR) is an NCRR/NIH Biomedical Technology Research Center established to develop computer-aided advanced microscopy for acquisition of structural and functional data in the dimensional range of 1nm3 to 100um3. With novel specimen staining methods, imaging instruments and computational capabilities, NCMIR researchers are addressing the next great biological challenges in the post-genomic age by situating proteins and macromolecular complexes in their cellular and tissue environments.

Core biological projects include development of new staining methods for intermediate voltage electron microscopy (IVEM) and for correlated light and IVEM analyses of specimens to examine the architecture of neuronal systems and the dynamics of subcellular processes. The Center's capabilities and research accomplishments in specimen preparation are augmented by the continued development of instruments and image processing facilities. Scientists at NCMIR have also focused on the development of technologies to integrate distributed resources and services around complicated scientific workflows. This group has an established record of collaborating with IT community leaders to provide biological to propel the development and refinement of software technologies for secure, authenticated access to disparate and distributed resources (instrumentation, computation, visualization, and data storage). A focus of this group has been the design and development of a comprehensive, platform independent, Grid-enabled system for researchers to perform end-to-end electron tomography and very-large field light microscopy. This Telescience Portal provides a centralized interface to a fully integrated collection of tools, infrastructure, and services necessary for a biologist to perform end-to-end electron tomography and ultra large-field light microscopy from any Internet capable location. For each workflow process, NCMIR researchers have a critical need to augment and accelerate the extraction of three-dimensional data products from generated volumes. To address this aim, SCI researchers will refine and extend the BioPSE environment to NCMIR researchers to provide targeted methods for automatic surface and volume rendering to minimize the time and labor intensive process of manual segmentation (a process that otherwise reduces experimental throughput). The focus of this technically oriented collaborative project is to strengthen the activity of the BioPSE software system with the Telescience Portal cyberinfrastructure used by NCMIR staff and project researchers.