pyabf 0.1.16

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

• Project Homepage: https://github.com/swharden/pyABF

• pyABF Cookbook: Getting Started

• pyABF Cookbook: Advanced Interactions with ABF Objects

• The Unofficial Guide to the ABF File Format

Quickstart

Display ABF Information:

import pyabf
abf=pyabf.ABF("filename.abf")
abf.info()

Access ABF Sweep Data:

import pyabf
abf=pyabf.ABF("filename.abf")
abf.setSweep(7)
print(abf.dataY, abf.units)
print(abf.dataC, abf.unitsCommand)
print(abf.dataX, abf.unitsTime)

Output:

[-47.729 -47.729 -47.76  ..., -42.542 -42.542 -42.572] mV
[ 0.  0.  0. ...,  0.  0.  0.] pA
[ 0.  0.  0. ...,  3.  3.  3.] seconds

Plot all sweeps with matplotlib:

import pyabf
import matplotlib.pyplot as plt

abf=pyabf.ABF("filename.abf")
for sweepNumber in abf.sweepList:
    abf.setSweep(sweepNumber)
    plt.plot(abf.dataX,abf.dataY)

plt.ylabel(abf.unitsLong)
plt.xlabel(abf.unitsTimeLong)
plt.margins(0,.1)
plt.show()

Output:

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