thorns 1

Description:

thorns 1

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With thorns you can analyze and display spike trains generated by
neurons. It can be useful for the analysis of experimental and
simulation data using Python. For example, you can easily calculate
peristimulus time histogram (PSTH), interspike time histogram (ISIH),
vector strength (VS), entrainment and visualize action potentials with
raster plot.
waves is a submodule with some useful signal processing and
generation functions, e.g. generate ramped tone, amplitude modulation
tone, FFT filter, set level (dB_SPL).
The software was originally developed during my PhD in the group of
Werner Hemmert at the TUM. It is oriented towards auditory
research, but it could be easily extended.

Usage
Don’t forget to check our IPython Notebook DEMO and scripts in the
examples directory!
Initialize and load spike trains:
import thorns as th
from thorns.datasets import load_anf_zilany2014

spike_trains = load_anf_zilany2014()
Calculate vector strength:
th.vector_strength(spike_trains, freq=1000)
Raster plot:
th.plot_raster(spike_trains)
th.show()
Generate and plot AM tone:
import thorns.waves as wv

sound = wv.amplitude_modulated_tone(
fs=48e3,
fm=100,
fc=1e3,
m=0.7,
duration=0.1,
)

wv.plot_signal(sound, fs=48e3)

wv.show()
You can also browse the API documentation at
https://pythonhosted.org/thorns/


Features

Analyzes and displays spike trains
Uses pandas.DataFrame as the main data container (spike trains,
results)
Handy signal processing and generating functions: thorns.waves
Map implementation with various backend (also parallel) and caching:
thorns.util.map()
Dumpdb: quickly dump map()’s results in one script and load from
another one: thorns.util.dumpdb(), thorns.util.loaddb()
Pure Python



Installation
In order to use thorns, you’ll need to install the following
dependencies first:

Python (2.7)
Numpy
Scipy
Pandas
PyTables / tables
Matplotlib
py-notify (optional, enables notifications)

Next, type in your command line:
pip install thorns


Contribute

Open tasks: TODO.org (best viewed in Emacs org-mode)
Issue Tracker: https://github.com/mrkrd/thorns/issues
Source Code: https://github.com/mrkrd/thorns



License
The project is licensed under the GNU General Public License v3 or
later (GPLv3+).