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

Project description

pyABF: a pure-Python ABF file reader

pyABF provides a Python interface to electrophysiology files in the Axon Binary Format (ABF). pyABF supports Python versions 3.6 and newer and does not use obscure libraries (just the standard libraries plus numpy and matplotlib). pyABF supports reading of ABF1 and ABF2 files, and can write ABF1 files.

pyABF electrophysiology data analysis with Python and Matplotlib

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()
pyABF Example

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/

pyABF Example

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