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Spike analysis software

Project Description

Spike analysis software

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Name:thorns
Author:Marek Rudnicki
Email:marek.rudnicki@tum.de
URL:https://github.com/mrkrd/thorns
Documentation:https://pythonhosted.org/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

Please, check our IPython Notebook DEMO.

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

  • Joerg Encke

Release history Release notifications

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0.10

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0.9

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0.7.3

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0.7.2

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0.7.1

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0.7

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0.6

This version
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0.5

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0.4

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0.3.1

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0.3

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0.2

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0.1

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Filename, size & hash SHA256 hash help File type Python version Upload date
thorns-0.5.tar.gz (37.8 kB) Copy SHA256 hash SHA256 Source None Aug 14, 2014

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