thorns
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Spike analysis software
thorns and waves
::
|||||||____|||||____||||______ |________||||_____|||______||__ |||_____|||||| ||||_____|||||||___________ ||||||||||__|_____THORNS
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.
.. _spike trains
: https://en.wikipedia.org/wiki/Spike_train
.. _Werner Hemmert
: https://www.ei.tum.de/en/bai/home/
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/
.. _DEMO: https://github.com/mrkrd/thorns/blob/master/examples/thorns_demo.ipynb .. _examples: examples
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
.. _TODO.org: TODO.org
License
The project is licensed under the GNU General Public License v3 or later (GPLv3+).