Abstract
Progress in experimental tools and design is allowing the acquisition of increasingly large datasets. Storage, manipulation and efficient analyses of such large amounts of data is now a primary issue. We present OpenElectrophy, an electrophysiological data- and analysis-sharing framework developed to fill this niche. It stores all experiment data and meta-data in a single central MySQL database, and provides a graphic user interface to visualize and explore the data, and a library of functions for user analysis scripting in Python. It implements multiple spike-sorting methods, and oscillation detection based on the ridge extraction methods due to Roux et al. (2007). OpenElectrophy is open source and is freely available for download at http://neuralensemble.org/trac/OpenElectrophy.
Highlights
Recent developments in electrophysiology experimental techniques have lead to increases in the amount of data produced
We present an example of the standard usage of OpenElectrophy to analyze extracellular local field potential (LFP) recordings and obtain information about action potential locking on LFP oscillation
In summary, we have presented OpenElectrophy, an open source project aimed at facilitating the management and manipulation of electrophysiological data along with experiment meta-data
Summary
Recent developments in electrophysiology experimental techniques have lead to increases in the amount of data produced. These projects were all written with the same primary goal as that of OpenElectrophy: to function as a framework for sharing analyses They provide most of the standard analysis tools and others developed more recently, all written in MATLAB, but they include no database framework or meta-data management. ORM to simplify read/write database access (see Section “A Typical Use-case” for an example of its use) This SQL mapper, a Python class included in OpenElectrophy, allows the user to declare a table structure with field names and types with only a few lines of code. Packages like Mlabwrap, rpy, cython or SciPy.weave enable to use pre-existent code from MATLAB, R, or C/C++ Employing these tools, the list of external modules that can be linked to OpenElectrophy to help write analysis scripts is long: the International Neuroinformatics Coordinating Facility provides a list of tools available for studying neural data. Details on how to use OpenElectrophy classes for scripting are available on the OpenElectrophy wiki page
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