Dec. 7, 2017 — Researchers with Carnegie Mellon’s Molecular Biosensor and Imaging Center (MBIC), the Pittsburgh Supercomputing Center (PSC) and the University of Pittsburgh’s Center for Biological Imaging (CBI) will help to usher in an era of open data research in neuroscience by building a confocal fluorescence microscopy data repository. The data archive will give researchers easy, searchable access to petabytes of existing data.
The project is funded by a $5 million, five-year grant from the National Institutes of Health’s (NIH’s) National Institute of Mental Health (MH114793) and is part of the federal BRAIN initiative.
“This grant is a testament to the fact that Pittsburgh is a leader in the fields of neuroscience, imaging and computer science,” said Marcel Bruchez, MBIC director, professor of biological sciences and chemistry at Carnegie Mellon and co-principal investigator of the grant. “By merging these disciplines, we will create a tool that helps the entire neuroscience community advance our understanding of the brain at an even faster pace.”
New imaging tools and technologies, like large-volume confocal fluorescence microscopy, have greatly accelerated neuroscience research in the past five years by allowing researchers to image large regions of the brain at such a high level of resolution that they can zoom in to the level of a single neuron or synapse, or zoom out to the level of the whole brain. These images, however, contain such a large amount of data that only a small part of one brain’s worth of data can be accessed at a time using a standard desktop computer. Additionally, images are often collected in different ways — at different resolutions, using different methodologies and different orientations. Comparing and combining data from multiple whole brains and datasets requires the power of supercomputing.
“PSC has a long experience with handling massive datasets for its users, as well as a deep skillset in processing microscopic images with high-performance computing,” said Alex Ropelewski, director of PSC’s Biomedical Applications Group and a co-principal investigator in the NIH grant. “This partnership with MBIC and CBI was a natural step in the ongoing collaborations between the institutions.”
The Pittsburgh-based team will bring together MBIC and CBI’s expertise in cell imaging and microscopy and pair it with the PSC’s long history of experience in biomedical supercomputing to create a system called the Brain Imaging Archive. Researchers will be able to submit their whole brain images, along with metadata about the images, to the archive. There the data will be indexed into a searchable system that can be accessed using the internet. Researchers can search the system to find existing data that will help them narrow down their research targets, making research much more efficient.
The Pittsburgh Supercomputing Center is a joint effort of Carnegie Mellon University and the University of Pittsburgh. Established in 1986, PSC is supported by several federal agencies, the Commonwealth of Pennsylvania and private industry, and is a leading partner in XSEDE (Extreme Science and Engineering Discovery Environment), the National Science Foundation cyberinfrastructure program.