Analysis of electrophysiological data recorded with the Axona or OpenEphys recording systems

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Project description

Synopsis

NB THIS IS NOW OUT OF DATE AS OF 2019_10_02

Tools for the analysis of electrophysiological data collected primarily with Axona recording products using Python.

Code Example

Main entry class is Trial contained in dacq2py_util i.e.

import dacq2py_util
T = dacq2py_util.Trial('/path/to/dataset/mytrial')

The "usual" Axona dataset includes the following files:

  • mytrial.set
  • mytrial.1
  • mytrial.2
  • mytrial.3
  • mytrial.4
  • mytrial.pos
  • mytrial.eeg

Note that you shouldn't specify a suffix when constructing the filename in the code example above.

You can now start analysing your data! i.e.

T.plotEEGPower()
T.plotMap(tetrode=1, cluster=4)

Motivation

Analysis using Axona's Tint cluster cutting program is great but limited. This extends that functionality.

Installation

Easiest way is with pip (under Linux, don't know how this works under other OS's):

pip install dacq2py

This should install all the pre-requisites, which are as follows:

  • numpy
  • scipy
  • matplotlib
  • scikits-learn
  • astropy (for NaN-friendly convolution)
  • skimage
  • mahotas

Optional packages include:

Download the files and extract to a folder and make sure it's on your Python path

API Reference

Most classes/ methods have some explanatory text. The files in the docs folder are extracted from that using standard Python tools.

Tests

To be implemented.

Contributors

Robin Hayman.

License

Do what you want license.

Project details

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Avatar for rhayman from gravatar.com rhayman

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