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!

Talk to Me: Nvidia Claims NLP Inference, Training Records

August 15, 2019

Nvidia says it’s achieved significant advances in conversation natural language processing (NLP) training and inference, enabling more complex, immediate-response interchanges between customers and chatbots. And the co Read more…

By Doug Black

Trump Administration and NIST Issue AI Standards Development Plan

August 14, 2019

Efforts to develop AI are gathering steam fast. On Monday, the White House issued a federal plan to help develop technical standards for AI following up on a mandate contained in the Administration’s AI Executive Order Read more…

By John Russell

Scientists to Tap Exascale Computing to Unlock the Mystery of our Accelerating Universe

August 14, 2019

The universe and everything in it roared to life with the Big Bang approximately 13.8 billion years ago. It has continued expanding ever since. While we have a good understanding of the early universe, its fate billions Read more…

By Rob Johnson

AWS Solution Channel

Efficiency and Cost-Optimization for HPC Workloads – AWS Batch and Amazon EC2 Spot Instances

High Performance Computing on AWS leverages the power of cloud computing and the extreme scale it offers to achieve optimal HPC price/performance. With AWS you can right size your services to meet exactly the capacity requirements you need without having to overprovision or compromise capacity. Read more…

HPE Extreme Performance Solutions

Bring the combined power of HPC and AI to your business transformation

FPGA (Field Programmable Gate Array) acceleration cards are not new, as they’ve been commercially available since 1984. Typically, the emphasis around FPGAs has centered on the fact that they’re programmable accelerators, and that they can truly offer workload specific hardware acceleration solutions without requiring custom silicon. Read more…

IBM Accelerated Insights

Cloudy with a Chance of Mainframes

[Connect with HPC users and learn new skills in the IBM Spectrum LSF User Community.]

Rapid rates of change sometimes result in unexpected bedfellows. Read more…

Argonne Supercomputer Accelerates Cancer Prediction Research

August 13, 2019

In the fight against cancer, early prediction, which drastically improves prognoses, is critical. Now, new research by a team from Northwestern University – and accelerated by supercomputing resources at Argonne Nation Read more…

By Oliver Peckham

Scientists to Tap Exascale Computing to Unlock the Mystery of our Accelerating Universe

August 14, 2019

The universe and everything in it roared to life with the Big Bang approximately 13.8 billion years ago. It has continued expanding ever since. While we have a Read more…

By Rob Johnson

AI is the Next Exascale – Rick Stevens on What that Means and Why It’s Important

August 13, 2019

Twelve years ago the Department of Energy (DOE) was just beginning to explore what an exascale computing program might look like and what it might accomplish. Today, DOE is repeating that process for AI, once again starting with science community town halls to gather input and stimulate conversation. The town hall program... Read more…

By Tiffany Trader and John Russell

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

Lenovo Drives Single-Socket Servers with AMD Epyc Rome CPUs

August 7, 2019

No summer doldrums here. As part of the AMD Epyc Rome launch event in San Francisco today, Lenovo announced two new single-socket servers, the ThinkSystem SR635 Read more…

By Doug Black

Building Diversity and Broader Engagement in the HPC Community

August 7, 2019

Increasing diversity and inclusion in HPC is a community-building effort. Representation of both issues and individuals matters - the more people see HPC in a w Read more…

By AJ Lauer

Xilinx vs. Intel: FPGA Market Leaders Launch Server Accelerator Cards

August 6, 2019

The two FPGA market leaders, Intel and Xilinx, both announced new accelerator cards this week designed to handle specialized, compute-intensive workloads and un Read more…

By Doug Black

Upcoming NSF Cyberinfrastructure Projects to Support ‘Long-Tail’ Users, AI and Big Data

August 5, 2019

The National Science Foundation is well positioned to support national priorities, as new NSF-funded HPC systems to come online in the upcoming year promise to Read more…

By Ken Chiacchia, Pittsburgh Supercomputing Center/XSEDE

High Performance (Potato) Chips

May 5, 2006

In this article, we focus on how Procter & Gamble is using high performance computing to create some common, everyday supermarket products. Tom Lange, a 27-year veteran of the company, tells us how P&G models products, processes and production systems for the betterment of consumer package goods. Read more…

By Michael Feldman

Supercomputer-Powered AI Tackles a Key Fusion Energy Challenge

August 7, 2019

Fusion energy is the Holy Grail of the energy world: low-radioactivity, low-waste, zero-carbon, high-output nuclear power that can run on hydrogen or lithium. T Read more…

By Oliver Peckham

Cray, AMD to Extend DOE’s Exascale Frontier

May 7, 2019

Cray and AMD are coming back to Oak Ridge National Laboratory to partner on the world’s largest and most expensive supercomputer. The Department of Energy’s Read more…

By Tiffany Trader

Graphene Surprises Again, This Time for Quantum Computing

May 8, 2019

Graphene is fascinating stuff with promise for use in a seeming endless number of applications. This month researchers from the University of Vienna and Institu Read more…

By John Russell

AMD Verifies Its Largest 7nm Chip Design in Ten Hours

June 5, 2019

AMD announced last week that its engineers had successfully executed the first physical verification of its largest 7nm chip design – in just ten hours. The AMD Radeon Instinct Vega20 – which boasts 13.2 billion transistors – was tested using a TSMC-certified Calibre nmDRC software platform from Mentor. Read more…

By Oliver Peckham

TSMC and Samsung Moving to 5nm; Whither Moore’s Law?

June 12, 2019

With reports that Taiwan Semiconductor Manufacturing Co. (TMSC) and Samsung are moving quickly to 5nm manufacturing, it’s a good time to again ponder whither goes the venerable Moore’s law. Shrinking feature size has of course been the primary hallmark of achieving Moore’s law... Read more…

By John Russell

Deep Learning Competitors Stalk Nvidia

May 14, 2019

There is no shortage of processing architectures emerging to accelerate deep learning workloads, with two more options emerging this week to challenge GPU leader Nvidia. First, Intel researchers claimed a new deep learning record for image classification on the ResNet-50 convolutional neural network. Separately, Israeli AI chip startup Hailo.ai... Read more…

By George Leopold

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
GOOGLE
GOOGLE
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
VERNE GLOBAL
VERNE GLOBAL

Nvidia Embraces Arm, Declares Intent to Accelerate All CPU Architectures

June 17, 2019

As the Top500 list was being announced at ISC in Frankfurt today with an upgraded petascale Arm supercomputer in the top third of the list, Nvidia announced its Read more…

By Tiffany Trader

Top500 Purely Petaflops; US Maintains Performance Lead

June 17, 2019

With the kick-off of the International Supercomputing Conference (ISC) in Frankfurt this morning, the 53rd Top500 list made its debut, and this one's for petafl Read more…

By Tiffany Trader

A Behind-the-Scenes Look at the Hardware That Powered the Black Hole Image

June 24, 2019

Two months ago, the first-ever image of a black hole took the internet by storm. A team of scientists took years to produce and verify the striking image – an Read more…

By Oliver Peckham

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

Cray – and the Cray Brand – to Be Positioned at Tip of HPE’s HPC Spear

May 22, 2019

More so than with most acquisitions of this kind, HPE’s purchase of Cray for $1.3 billion, announced last week, seems to have elements of that overused, often Read more…

By Doug Black and Tiffany Trader

Chinese Company Sugon Placed on US ‘Entity List’ After Strong Showing at International Supercomputing Conference

June 26, 2019

After more than a decade of advancing its supercomputing prowess, operating the world’s most powerful supercomputer from June 2013 to June 2018, China is keep Read more…

By Tiffany Trader

In Wake of Nvidia-Mellanox: Xilinx to Acquire Solarflare

April 25, 2019

With echoes of Nvidia’s recent acquisition of Mellanox, FPGA maker Xilinx has announced a definitive agreement to acquire Solarflare Communications, provider Read more…

By Doug Black

Qualcomm Invests in RISC-V Startup SiFive

June 7, 2019

Investors are zeroing in on the open standard RISC-V instruction set architecture and the processor intellectual property being developed by a batch of high-flying chip startups. Last fall, Esperanto Technologies announced a $58 million funding round. Read more…

By George Leopold

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