PUBLICATION
Mapping brain activity at scale with cluster computing
- Authors
- Freeman, J., Vladimirov, N., Kawashima, T., Mu, Y., Sofroniew, N.J., Bennett, D.V., Rosen, J., Yang, C.T., Looger, L.L., Ahrens, M.B.
- ID
- ZDB-PUB-140730-8
- Date
- 2014
- Source
- Nature Methods 11(9): 941-50 (Journal)
- Registered Authors
- Ahrens, Misha, Bennett, Davis, Kawashima, Takashi, Mu, Yu, Vladimirov, Nikita, Yang, Chao-Tsung
- Keywords
- none
- MeSH Terms
-
- Database Management Systems
- Data Interpretation, Statistical
- Action Potentials/physiology*
- Nerve Net/physiology*
- Computing Methodologies
- Models, Neurological*
- Humans
- Programming Languages
- Databases, Factual
- Brain Mapping/methods*
- Computer Simulation
- Software*
- Neurons/physiology*
- Animals
- Information Storage and Retrieval/methods*
- Brain/physiology
- PubMed
- 25068736 Full text @ Nat. Methods
Citation
Freeman, J., Vladimirov, N., Kawashima, T., Mu, Y., Sofroniew, N.J., Bennett, D.V., Rosen, J., Yang, C.T., Looger, L.L., Ahrens, M.B. (2014) Mapping brain activity at scale with cluster computing. Nature Methods. 11(9):941-50.
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping