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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.


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).

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:


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()

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)


Check the docs for more examples.

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