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Simple viewers for ephys signals, events, video and more

Project description

Simple viewers for ephys signals, events, video and more

Distributions:PyPI Anaconda Cloud
Source Code:GitHub conda-forge Feedstock
Docs Status:Documentation Status

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ephyviewer is a Python library based on pyqtgraph for building custom viewers for electrophysiological signals, video, events, epochs, spike trains, data tables, and time-frequency representations of signals. It also provides an epoch encoder for creating annotations.

Screenshot

ephyviewer can be used at two levels: standalone app and library.

For an example of an application that utilizes ephyviewer’s capabilities as a library, see the neurotic app and this paper:

Gill, J. P., Garcia, S., Ting, L. H., Wu, M., & Chiel, H. J. (2020). neurotic: Neuroscience Tool for Interactive Characterization. eNeuro, 7(3). https://doi.org/10.1523/ENEURO.0085-20.2020

Standalone application

The standalone app works with file types supported by Neo’s RawIO interface (Axograph, Axon, Blackrock, BrainVision, Neuralynx, NeuroExplorer, Plexon, Spike2, Tdt, etc.; see the documentation for neo.rawio for the full list).

Launch it from the console and use the menu to select a data file:

ephyviewer

Alternatively, launch it from the console with a filename (and optionally the format):

ephyviewer File_axon_1.abf
ephyviewer File_axon_1.abf -f Axon

Library for designing custom viewers for ephys datasets

Build viewers using code like this:

import ephyviewer
import numpy as np

app = ephyviewer.mkQApp()

#signals
sigs = np.random.rand(100000,16)
sample_rate = 1000.
t_start = 0.
view1 = ephyviewer.TraceViewer.from_numpy(sigs, sample_rate, t_start, 'Signals')

win = ephyviewer.MainViewer(debug=True, show_auto_scale=True)
win.add_view(view1)
win.show()

app.exec_()

Check the docs for more examples.

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