CMU, PSC and Pitt to Build Brain Data Repository

December 7, 2017

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.

About PSC

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.


Source: PSC

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

InfiniBand Still Tops in Supercomputing

July 19, 2018

In the competitive global HPC landscape, system and processor vendors, nations and end user sites certainly get a lot of attention--deservedly so--but more than ever, the network plays a crucial role. While fast, perform Read more…

By Tiffany Trader

HPC for Life: Genomics, Brain Research, and Beyond

July 19, 2018

During the past few decades, the life sciences have witnessed one landmark discovery after another with the aid of HPC, paving the way toward a new era of personalized treatments based on an individual’s genetic makeup Read more…

By Warren Froelich

WCRP’s New Strategic Plan for Climate Research Highlights the Importance of HPC

July 19, 2018

As climate modeling increasingly leverages exascale computing and researchers warn of an impending computing gap in climate research, the World Climate Research Programme (WCRP) is developing its new Strategic Plan – and high-performance computing is slated to play a critical role. Read more…

By Oliver Peckham

HPE Extreme Performance Solutions

Introducing the First Integrated System Management Software for HPC Clusters from HPE

How do you manage your complex, growing cluster environments? Answer that big challenge with the new HPC cluster management solution: HPE Performance Cluster Manager. Read more…

IBM Accelerated Insights

Are Your Software Licenses Impeding Your Productivity?

In my previous article, Improving chip yield rates with cognitive manufacturing, I highlighted the costs associated with semiconductor manufacturing, and how cognitive methods can yield benefits in both design and manufacture.  Read more…

U.S. Exascale Computing Project Releases Software Technology Progress Report

July 19, 2018

As is often noted the race to exascale computing isn’t just about hardware. This week the U.S. Exascale Computing Project (ECP) released its latest Software Technology (ST) Capability Assessment Report detailing progress so far. Read more…

By John Russell

InfiniBand Still Tops in Supercomputing

July 19, 2018

In the competitive global HPC landscape, system and processor vendors, nations and end user sites certainly get a lot of attention--deservedly so--but more than Read more…

By Tiffany Trader

HPC for Life: Genomics, Brain Research, and Beyond

July 19, 2018

During the past few decades, the life sciences have witnessed one landmark discovery after another with the aid of HPC, paving the way toward a new era of perso Read more…

By Warren Froelich

D-Wave Breaks New Ground in Quantum Simulation

July 16, 2018

Last Friday D-Wave scientists and colleagues published work in Science which they say represents the first fulfillment of Richard Feynman’s 1982 notion that Read more…

By John Russell

AI Thought Leaders on Capitol Hill

July 14, 2018

On Thursday, July 12, the House Committee on Science, Space, and Technology heard from four academic and industry leaders – representatives from Berkeley Lab, Argonne Lab, GE Global Research and Carnegie Mellon University – on the opportunities springing from the intersection of machine learning and advanced-scale computing. Read more…

By Tiffany Trader

HPC Serves as a ‘Rosetta Stone’ for the Information Age

July 12, 2018

In an age defined and transformed by its data, several large-scale scientific instruments around the globe might be viewed as a ‘mother lode’ of precious data. With names seemingly created for a ‘techno-speak’ glossary, these interferometers, cyclotrons, sequencers, solenoids, satellite altimeters, and cryo-electron microscopes are churning out data in previously unthinkable and seemingly incomprehensible quantities -- billions, trillions and quadrillions of bits and bytes of electro-magnetic code. Read more…

By Warren Froelich

Tsinghua Powers Through ISC18 Field

July 10, 2018

Tsinghua University topped all other competitors at the ISC18 Student Cluster Competition with an overall score of 88.43 out of 100. This gives Tsinghua their s Read more…

By Dan Olds

HPE, EPFL Launch Blue Brain 5 Supercomputer

July 10, 2018

HPE and the Ecole Polytechnique Federale de Lausannne (EPFL) Blue Brain Project yesterday introduced Blue Brain 5, a new supercomputer built by HPE, which displ Read more…

By John Russell

Pumping New Life into HPC Clusters, the Case for Liquid Cooling

July 10, 2018

High Performance Computing (HPC) faces some daunting challenges in the coming years as traditional, industry-standard systems push the boundaries of data center Read more…

By Scott Tease

Leading Solution Providers

SC17 Booth Video Tours Playlist

Altair @ SC17

Altair

AMD @ SC17

AMD

ASRock Rack @ SC17

ASRock Rack

CEJN @ SC17

CEJN

DDN Storage @ SC17

DDN Storage

Huawei @ SC17

Huawei

IBM @ SC17

IBM

IBM Power Systems @ SC17

IBM Power Systems

Intel @ SC17

Intel

Lenovo @ SC17

Lenovo

Mellanox Technologies @ SC17

Mellanox Technologies

Microsoft @ SC17

Microsoft

Penguin Computing @ SC17

Penguin Computing

Pure Storage @ SC17

Pure Storage

Supericro @ SC17

Supericro

Tyan @ SC17

Tyan

Univa @ SC17

Univa

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This