pyabf 2.3.8

Python library for reading files in Axon Binary Format (ABF)

pyABF: a pure-Python ABF file reader

pyABF provides a Python interface to electrophysiology files in the Axon Binary Format (ABF). pyABF supports Python 3 and does not use obscure libraries (just numpy and matplotlib). pyABF supports reading ABF1 and ABF2 files and can write ABF1 files.

Quickstart

Install or upgrade pyABF:

pip install --upgrade pyabf

Access ABF sweep data:

import pyabf
abf = pyabf.ABF("demo.abf")
abf.setSweep(sweepNumber=3, channel=0)
print(abf.sweepY) # displays sweep data (ADC)
print(abf.sweepX) # displays sweep times (seconds)
print(abf.sweepC) # displays command waveform (DAC)

Plot a sweep with Matplotlib:

import pyabf
import matplotlib.pyplot as plt
abf = pyabf.ABF("demo.abf")
abf.setSweep(14)
plt.plot(abf.sweepX, abf.sweepY)
plt.show()

Additional Examples

Full pyabf API documentation, additional code examples, a pyabf cookbook, and low-level information about the ABF file format can be found at the pyABF project homepage: http://swharden.com/pyabf/