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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 2.7 and Python 3.6+ 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(3)
print(abf.sweepY) # sweep data (ADC)
print(abf.sweepC) # sweep command (DAC)
print(abf.sweepX) # sweep times (seconds)

Plot a sweep with Matplotlib:

import matplotlib.pyplot as plt
import pyabf
abf = pyabf.ABF("17o05028_ic_steps.abf")
abf.setSweep(14)
plt.plot(abf.sweepX, abf.sweepY)
plt.show()
pyABF Example

Get fancy with Matplotlib:

import matplotlib.pyplot as plt
import pyabf
abf = pyabf.ABF("sample.abf")

plt.figure(figsize=(8, 5))
for sweepNumber in range(abf.sweepCount)[::5]:
    abf.setSweep(sweepNumber)
    plt.plot(abf.sweepX,abf.sweepY,alpha=.5,label="sweep %d"%(sweepNumber))

plt.legend()
plt.ylabel(abf.sweepLabelY)
plt.xlabel(abf.sweepLabelX)
plt.title("pyABF and Matplotlib are a great pair!")
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: https://github.com/swharden/pyABF

pyABF Example

Citing pyABF

If the pyABF module facilitated your research, consider citing this project by name so it can benefit others too:

“Computational analysis of electrophysiological recordings was performed with custom software written for this project using Python 3.6 and the pyABF module.”

Feature Requests / Unsupported ABF Files

If you have ABF files which are unsupported (or read incorrectly) by this software, it is likely due to a use case we have not run across yet, so let us know about it! We can only develop and test this software against ABF files we have access to, so if you’re interested in having your ABF file supported send the primary author an email (and the ABF file you are trying to analyze) and we will investigate it. If a solution is reached the pyabf package will be updated so everyone can benefit from the change. We can only develop for (and test against) ABFs we have access to, so we really appreciate your contributions!


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