title: Mapping brain activity at scale with cluster computing.
abstract: Understanding brain function requires monitoring and interpreting the activity of large networks of neurons during behavior. Advances in recording technology are greatly increasing the size and complexity of neural data. Analyzing such data will pose a fundamental bottleneck for neuroscience. We present a library of analytical tools called Thunder built on the open-source Apache Spark platform for large-scale distributed computing. The library implements a variety of univariate and multivariate analyses with a modular, extendable structure well-suited to interactive exploration and analysis development. We demonstrate how these analyses find structure in large-scale neural data, including whole-brain light-sheet imaging data from fictively behaving larval zebrafish, and two-photon imaging data from behaving mouse. The analyses relate neuronal responses to sensory input and behavior, run in minutes or less and can be used on a private cluster or in the cloud. Our open-source framework thus holds promise for turning brain activity mapping efforts into biological insights.
authors: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors: Jeremy
authors: J
authors: Freeman
authors: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors: Nikita
authors: N
authors: Vladimirov
authors: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors: Takashi
authors: T
authors: Kawashima
authors: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors: Yu
authors: Y
authors: Mu
authors: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors: Nicholas J
authors: NJ
authors: Sofroniew
authors: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors: Davis V
authors: DV
authors: Bennett
authors: University of California Berkeley, Computer Science Division, Berkeley, California, USA.
authors: Joshua
authors: J
authors: Rosen
authors: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors: Chao-Tsung
authors: CT
authors: Yang
authors: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors: Loren L
authors: LL
authors: Looger
authors: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors: Misha B
authors: MB
authors: Ahrens
mesh_terms: D000200:Action Potentials / Q000502:physiology*; D000818:Animals; D001921:Brain / Q000502:physiology; D001931:Brain Mapping / Q000379:methods*; D003198:Computer Simulation; D003205:Computing Methodologies; D003627:Data Interpretation, Statistical; D003628:Database Management Systems; D016208:Databases, Factual; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D008959:Models, Neurological; D009415:Nerve Net / Q000502:physiology*; D009474:Neurons / Q000502:physiology*; D011381:Programming Languages; D012984:Software