Original Research Article
Python for large-scale electrophysiology
1 Ophthalmology and Visual Sciences, University of British Columbia, Canada
2 Redwood Center for Theoretical Neuroscience, University of California, USA
2 Redwood Center for Theoretical Neuroscience, University of California, USA
Electrophysiology is increasingly moving towards highly parallel recording techniques which generate large data sets. We record extracellularly in vivo in cat and rat visual cortex with 54 channel silicon polytrodes, under time-locked visual stimulation, from localized neuronal populations within a cortical column. To help deal with the complexity of generating and analyzing these data, we used the Python programming language to develop three software projects: one for temporally precise visual stimulus generation ("dimstim"); one for electrophysiological waveform visualization and spike sorting ("spyke"); and one for spike train and stimulus analysis ("neuropy"). All three are open source and available for download (http://swindale.ecc.ubc.ca/code). The requirements and solutions for these projects differed greatly, yet we found Python to be well suited for all three. Here we present our software as a showcase of the extensive capabilities of Python in neuroscience.
Keywords: Python, polytrodes, visual cortex
Copyright: © Spacek, Blanche and Swindale. This is an open-access article subject to an exclusive license agreement between the authors and the Frontiers Research Foundation, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited.
*Correspondence: Martin Spacek, Department of Ophthalmology and Visual Sciences, University of British Columbia, 2550 Willow Street, Vancouver, BC, V5Z 3N9, Canada. frontiers@mspacek.mm.st
Citation: Spacek M, Blanche T and Swindale N (2008) Python for large-scale electrophysiology. Front. Neuroinform. doi:10.3389/neuro.11.009.2008
Received: 18 September 2008; paper pending published: 04 November 2008; accepted: 19 December 2008;
Edited by:
Rolf Kötter, Radboud University Nijmegen, The Netherlands
Reviewed by:
Gaute T. Einevoll, Norwegian University of Life Sciences, Norway
*Correspondence: Martin Spacek, Department of Ophthalmology and Visual Sciences, University of British Columbia, 2550 Willow Street, Vancouver, BC, V5Z 3N9, Canada. frontiers@mspacek.mm.st
