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Python package for parsing Open Ephys data.

Project description

Build Status Project Status: Active - The project has reached a stable, usable state and is being actively developed. codecov

pyopenephys

Python reader for Open Ephys.

Installation

In order to install the pyopenephys package, open a terminal and run:

pip install pyopenephys

If you want to install from sources and get the latest updates, clone the repo and install locally:

git clone https://github.com/CINPLA/pyopenephys
cd pyopenephys
python setup.py install 
# use 'python setup.py develop' to install fixed bugs 

Basic Usage

Pyopenephys allows the user to load data recorded with Open Ephys. Currently, only the binary (recommended) and openephys (support for this format will be dropped in future releases) are supported.

The first step is creating a File object. It only requires to pass the paht to the recording folder.

import pyopenephys
file = pyopenephys.File("path-to-recording-folder") 

The file object contains the different experiments (corresponding to different settings files) and each experiment contains a set of recordings.

# all experiments
experiments = file.experiments
print(len(experiments))

# recordings of first experiment
experiment = experiments[0]
recordings = experiment.recordings
print(len(experiments))

# access first recording
recording = recordings[0]

Experiments store some useful information:

  • experiment.datetime contains the starting date and time of the experiment creation
  • experiment.sig_chain is a dictionary containing the processors and nodes in the signal chain
  • experiment.settings is a dictionary with the parsed setting.xml file
  • experiment.acquisition_system contains the system used to input continuous data (e.g. 'Rhythm FPGA')

Recordings contain the actual data:

  • recording.duration is the duration of the recording (in seconds)
  • recording.sample_rate is the sampling frequency (in Hz)
  • recording.analog_signals is list of AnalogSignal objects, which in turn have a signal, times (in s), and channel_id fields.
  • recording.events is list of EventData objects, which in turn have a times (in s), channels, channel_states, full_words, processor, node_id, and metadata fields.
  • recording.tracking is list of TrackingData objects , which in turn have a times (in s), x, y, width, height, channels, and metadata fields. Tracking data are recorded with the Tracking plugin (https://github.com/CINPLA/tracking-plugin) and are save in binary format only (not in openephys format).
  • recording.spiketrains is list of SpikeTrain objects, which in turn have a times, waveforms, electrode_indices, clusters and metadata fields. Spiketrains are saved by the Spike Viewer sink in the Open Ephys GUI, in combination with either the Spike Detector and Spike Viewer.

With a few lines of code, the data and relevant information can be easily parsed and accessed:

import pyopenephys
import matplotlib.pylab as plt

file = pyopenephys.File("path-to-recording-folder") 
# experiment 1 (0 in Python)
experiment = file.experiments[0]
# recording 1 
recording = experiment.recordings[0]

print('Duration: ', recording.duration)
print('Sampling Rate: ', recording.sample_rate)

analog_signals = recording.analog_signals
events_data = recording.events
spiketrains = recording.spiketrains
# tracking_data are accessible only using binary format
tracking_data = recording.tracking

# plot analog signal of channel 4
signals = analog_signals[0]
fig_an, ax_an = plt.subplots()
ax_an.plot(signals.times, signals.signal[3])

# plot raster for spike trains
fig_sp, ax_sp = plt.subplots()
for i_s, sp in enumerate(spiketrains):
    ax_sp.plot(sp.times, i_s*np.ones(len(sp.times)), '|')

plt.show()

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