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New tools help neuroscientists analyze 'big data'
Date:7/27/2014

for large-scale computing across industry, Freeman says. Spark's capabilities for data caching eliminates the bottleneck of loading a complete data set for all but the initial step, making it well-suited for interactive, exploratory analysis, and for complex algorithms requiring repeated operations on the same data. And Spark's elegant and versatile application programming interfaces (APIs) help simplify development. Thunder uses the Python API, which Freeman hopes will make it particularly easy for others to adopt, given Python's increasing use in neuroscience and data science.

To make Spark suitable for analyzing a broad range of neuroscience data information about connectivity and activity collected from different organisms and with different techniques Freeman first developed standardized representations of data that were amenable to distributed computing. He then worked to express typical neuroscience workflows into the computational language of Spark.

From there, he says, the biological questions that he and his colleagues were curious about drove development. "We started with our questions about the biology, then came up with the analyses and developed the tools," he says.

The result is a modular set of tools that will expand as the Janelia team -- and the neuroscience community -- add new components. "The analyses we developed are building blocks," says Ahrens. "The development of new analyses for interpreting large-scale recording is an active field and goes hand-in-hand with the development of resources for large-scale computing and imaging. The algorithms in our paper are a starting point."

Using Thunder, Freeman, Ahrens, and their colleagues analyzed images of the brain in minutes, interacting with and revising analyses without the lengthy delays associated with previous methods. In images taken of a mouse brain with a two-photon microscope, for example, the team found cells in the brain whose activity varied with
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Contact: Jim Keeley
keeleyj@hhmi.org
301-215-8858
Howard Hughes Medical Institute
Source:Eurekalert

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