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Aurora Supercomputer to Drive Brain Map Construction in the U.S.

The U.S. Department of Energy’s (DOE) Argonne National Laboratory will be home to one of the nation’s first exascale supercomputers when Aurora arrives in 2022. With access to pre-production hardware and software, these researchers are among the first in the world to utilise exascale technologies for science.

Using far more advanced imaging techniques than those of their earlier contemporaries, the researchers are working to develop a brain connectome, an accurate map that lays out every connection between every neuron and the precise location of the associated dendrites, axons and synapses that help form the communications or signalling pathways of a brain.

The project is a wide-ranging collaboration between computer scientists and neuroscientists, and academic and corporate research institutions. The research was impossible to be done until the advancement of ultra-high-resolution imaging techniques and more powerful supercomputing resources. These technologies allow for finer resolution of microscopic anatomy and the ability to wrangle the sheer size of the data.

Only the computing power of an Aurora, an exascale machine capable of performing a billion billion calculations per second, will meet the near-term challenges in brain mapping. Currently, without that power, the team is working on smaller brain samples, some of them only one cubic millimetre. Even this small mass of neurological matter can generate a petabyte of data. With the goal of one day mapping a whole mouse brain, about a centimetre cubed, the amount of data would increase by a thousandfold at a reasonable resolution.

If we do not improve today’s technology, the compute time for a whole mouse brain would be something like 1,000,000 days of work on current supercomputers. Using all of Aurora, if everything worked beautifully, it could still take 1,000 days. So, the problem of reconstructing a brain connectome requires exascale resources and beyond.

– Argonne Senior Computer Scientist

Working primarily with mouse brain samples, the team is developing a computational pipeline to analyse the data obtained from a complicated process of staining, slicing and imaging. The process begins with samples of brain tissue which are stained with heavy metals to provide visual contrast and then sliced extremely thin with a precision cutting tool called an ultramicrotome. These slices are mounted for imaging with Argonne’s massive-data-producing electron microscope, generating a collection of smaller images, or tiles.

The resulting tiles have to be digitally reassembled, or stitched together, to reconstruct the slice. Each of those slices has to be stacked and aligned properly to reproduce the 3D volume. At this point, neurons are traced through the 3D volume by a process known as segmentation to identify neuron shape and synaptic connectivity.

This segmentation step relies on an Artificial Intelligence technique called a convolutional neural network; in this case, a type of network developed by Google for the reconstruction of neural circuits from electron microscopy images of the brain. While it has demonstrated better performance than past approaches, the technique also comes with a high computational cost when applied to large volumes.

Using supercomputers for this work demands efficiency at every scale, from distributing large datasets across the compute nodes, to running algorithms on the individual nodes with high-bandwidth communication, to writing the final results to the parallel file system. Large-scale analysis of the results truly starts to probe questions about what emerges from the neurons and their connectivity.

The team’s preparations for exascale will serve as a benefit to other exascale system users. For example, the algorithms they are developing for their electron microscopy data will find applications with X-ray data. With the right tools in place and exascale computing at hand, the development and analysis of large-scale, precision connectomes will help researchers fill the gaps in some age-old questions.

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Qlik’s vision is a data-literate world, where everyone can use data and analytics to improve decision-making and solve their most challenging problems. A private company, Qlik offers real-time data integration and analytics solutions, powered by Qlik Cloud, to close the gaps between data, insights and action. By transforming data into Active Intelligence, businesses can drive better decisions, improve revenue and profitability, and optimize customer relationships. Qlik serves more than 38,000 active customers in over 100 countries.

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CTC Global Singapore, a premier end-to-end IT solutions provider, is a fully owned subsidiary of ITOCHU Techno-Solutions Corporation (CTC) and ITOCHU Corporation.

Since 1972, CTC has established itself as one of the country’s top IT solutions providers. With 50 years of experience, headed by an experienced management team and staffed by over 200 qualified IT professionals, we support organizations with integrated IT solutions expertise in Autonomous IT, Cyber Security, Digital Transformation, Enterprise Cloud Infrastructure, Workplace Modernization and Professional Services.

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Planview has one mission: to build the future of connected work. Our solutions enable organizations to connect the business from ideas to impact, empowering companies to accelerate the achievement of what matters most. Planview’s full spectrum of Portfolio Management and Work Management solutions creates an organizational focus on the strategic outcomes that matter and empowers teams to deliver their best work, no matter how they work. The comprehensive Planview platform and enterprise success model enables customers to deliver innovative, competitive products, services, and customer experiences. Headquartered in Austin, Texas, with locations around the world, Planview has more than 1,300 employees supporting 4,500 customers and 2.6 million users worldwide. For more information, visit www.planview.com.

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SIRIM is a premier industrial research and technology organisation in Malaysia, wholly-owned by the Minister​ of Finance Incorporated. With over forty years of experience and expertise, SIRIM is mandated as the machinery for research and technology development, and the national champion of quality. SIRIM has always played a major role in the development of the country’s private sector. By tapping into our expertise and knowledge base, we focus on developing new technologies and improvements in the manufacturing, technology and services sectors. We nurture Small Medium Enterprises (SME) growth with solutions for technology penetration and upgrading, making it an ideal technology partner for SMEs.

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HashiCorp provides infrastructure automation software for multi-cloud environments, enabling enterprises to unlock a common cloud operating model to provision, secure, connect, and run any application on any infrastructure. HashiCorp tools allow organizations to deliver applications faster by helping enterprises transition from manual processes and ITIL practices to self-service automation and DevOps practices. 

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IBM is a leading global hybrid cloud and AI, and business services provider. We help clients in more than 175 countries capitalize on insights from their data, streamline business processes, reduce costs and gain the competitive edge in their industries. Nearly 3,000 government and corporate entities in critical infrastructure areas such as financial services, telecommunications and healthcare rely on IBM’s hybrid cloud platform and Red Hat OpenShift to affect their digital transformations quickly, efficiently and securely. IBM’s breakthrough innovations in AI, quantum computing, industry-specific cloud solutions and business services deliver open and flexible options to our clients. All of this is backed by IBM’s legendary commitment to trust, transparency, responsibility, inclusivity and service.

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