pyabf 2.0.21

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

pyABF provides a Python interface to files in the Axon Binary Format (ABF)

• Project Homepage

• Getting Started with pyABF

• Unofficial Guide to the ABF File Format

Quickstart

Access Sweep Data:

import pyabf
abf = pyabf.ABF("demo.abf")
abf.setSweep(3) # sweeps start at 0
print(abf.sweepY) # sweep data (ADC)
print(abf.sweepC) # sweep command (DAC)
print(abf.sweepX) # sweep times (seconds)

Plot a Single Sweep:

import matplotlib.pyplot as plt
import pyabf
abf = pyabf.ABF("17o05028_ic_steps.abf")
abf.setSweep(14)
plt.plot(abf.sweepX, abf.sweepY, lw=.5)
plt.show()

Create Fancy Plots with Matplotlib:

import matplotlib.pyplot as plt
import pyabf
abf = pyabf.ABF("17o05028_ic_steps.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=f"sweep {sweepNumber+1}")

plt.margins(0, .1)
plt.legend()
plt.ylabel(abf.sweepLabelY)
plt.xlabel(abf.sweepLabelX)
plt.title(abf.abfID)
plt.tight_layout()
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: https://github.com/swharden/pyABF