ephysio 1.0.9

Tools for reading ephys data

ephysio

Python code for reading ephys files

openEphysIO

This module provides convenient access to continuous and event data saved by OpenEphys. For instance:

from ephysio import openEphysIO
import matplotlib.pyplot as plt

ldr = openEphysIO.Loader("/path/to/data")

# first probe
strm = ldr.spikestreams()[0] 

# time x channel map of the data
dat = ldr.data(strm) 

# sampling rate in Hz
fs_Hz = ldr.samplingrate(strm) 
STIMMARKERCHANNEL = 2

# time stamps of events in channel 2 on the NIDAQ, translated to neuropixel time
evts = ldr.nidaqevents()[STIMMARKERCHANNEL] 
CHANNEL = 100
STIMNO = 10

# Start time of event #10
s0 = evts[STIMNO, 0] 

# prepare to receive 100 ms of data
ds = np.arange(int(.1*fs_Hz)) 

# 100 ms of data following the stimulus 
response = dat[s0:s0+ds, CHANNEL] 

# plot data with time in ms on x-axis
plt.plot(ds*1000/fs_Hz, response) 

Much more documentation is included in the module itself. Most users will want to use the Loader class rather than the various other functions.

Credits

Developed and tested by DAW and Frank Lanfranchi.