skip to navigation
skip to content

Not Logged In

thorns 0.3.1

Spike analysis software

Package Documentation

Latest Version: 0.7.1

Spike analysis software

__|________|_____|_|_|___|_____|____||_____|_____|_____|____|_____|___||______
_|_______________________|______|_________|_______|_____|____|__|________|_|__
_____|___|__|_____|_______|____|_________________________|__|_________|_______
___|_______|_____|______|_____|_______|__|___|________|______|___|____________
__|__|_______|_____|__|___|______|________|______|______|_____|_______THORNS__
Name:thorns
Author:Marek Rudnicki
Email:marek.rudnicki@tum.de
URL:https://github.com/mrkrd/thorns
License:GNU General Public License v3 or later (GPLv3+)

Description

With thorns you can analyze and display spike trains generated by neurons. It can be useful for both 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).

I developed the package 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

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()

Requirements

  • Python (2.7)
  • Numpy
  • Scipy
  • Pandas
  • Matplotlib

Installation

Quick install:

pip install thorns

Contributors

  • Jörg Encke
 
File Type Py Version Uploaded on Size
thorns-0.3.1.tar.gz (md5) Source 2014-06-28 36KB
  • Downloads (All Versions):
  • 10 downloads in the last day
  • 123 downloads in the last week
  • 543 downloads in the last month