neuropy is a Python application for interactive analysis of neuronal spike, LFP, and stimulus data.
The user-facing data object hierarchy looks like this:
level:
Animal 1
|
Track 2 Track
| |
Recording 3 TrackSort
/ | \ |
Sort LFP Experiment 4 TrackNeuron
|
Neuron 5
Once data are loaded, they can be accessed in various ways:
animal.track.recording
animal.tr[trackid].r[recordingid]
recording.n[neuronid]
For example, to plot a population raster plot of all active cells in recording 5 of track 1 of animal example1, you can type:
example1.tr1.r05.praster()
Different object types have different analysis methods associated with them.
Thanks to IPython, tab completion should help you discover
analysis methods, and typing ?
after the method name or simply typing the opening
parenthesis should give you a docstring.
As for internal variable scope, this is how things work:
Main Qt event loop creates a
NeuropyWindow which runs an
IPython session which imports
neuropy modules
So, something like get_ipython()
only works from within those neuropy modules
that have been imported during the IPython session, but not in any of
NeuropyWindow
's methods.
Some more details are available in Appendix C.3 of my thesis.
Dependencies:
neuropy requires recent versions of the following to be installed:
- Python (3.x, 2.x no longer supported)
- IPython 5.3.0
- numpy
- scipy
- matplotlib
- PyQt4 (PySide will probably work too, but is untested)
- Cython
Optional:
To ensure that the Qt v2
API is used by
IPython, run export QT_API=pyqt
at the command line before running neuropy, or add it to
your .bashrc
or .bash_aliases
file.
Some analyses assume the use of custom matplotlib default settings in the included matplotlibrc file.
neuropy is developed in Xubuntu 14.04. It should work in other Linux distributions. In principle, it should also work in Windows and OSX.
An older version is described in the paper [Python for large-scale electrophysiology] (http://www.frontiersin.org/Neuroinformatics/10.3389/neuro.11.009.2008/abstract).
To run:
$ python main.py # in the neuropy folder
To install for use as a library:
$ python setup.py install