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LBNL to Help Create Standard 3D Neuron Model

Researchers at Lawrence Berkeley National Laboratory are contributing to the BigNeuron project, a community effort to define and advance the state of the art of single neuron reconstruction and analysis and create a common platform for analyzing 3D neuronal structure.

Over the years, dozens of imaging paradigms and algorithms have been created for visualizing the 3D structure of neurons—leading to a variety of disparate datasets in the field. But neuroscientists widely agree that to solve the mysteries of the brain, they need to cross-compare these datasets. That’s why many of the field’s brightest minds are participating in BigNeuron.

In an attempt to find a standard neuron reconstruction algorithm, BigNeuron will sponsor a series of international hackathons and workshops where contending algorithms will be ported onto a common software platform to analyze neuronal physical structure using the same core dataset. All ported algorithms will be bench-tested at Department of Energy supercomputing centers—including the National Energy Research Scientific Computing Center (NERSC) at the Lawrence Berkeley National Laboratory (Berkeley Lab) and the Oak Ridge Leadership Computing Facility (OLCF) at the Oak Ridge National Laboratory (ORNL)—as well as Human Brain Project supercomputing centers, allowing the community to standardize optimal protocols for labeling, visualizing and analyzing neuronal structure and key biological features.

The data generated by these benchmark runs will be used to develop a comprehensive annotated database of complex neuronal morphology, generate a searchable tool for discovering annotated and unique characteristics of neuronal morphology and lay the groundwork for potentially integrating this tool with large-scale data sets linking form to neuronal function. In addition, researchers will be able to access it via the Collaborative Research in Computational Neuroscience (CRCNS) data-sharing portal hosted by NERSC, which allows neuroscience researchers worldwide to easily share files without having to download any special software.

BigNeuron highlights NERSC’s strengths as a unified facility where people can run sophisticated data analytics algorithms and simulations and a worldwide community of researchers can easily access the results over the Internet,” says Prabhat, leader of NERSC’s Data and Analytics Services Group and BigNeuron collaborator.

The Allen Institute for Brain Science is coordinating the BigNeuron effort; read their press release.

Source: NERSC

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