Python library for reading files in Axon Binary Format (ABF)
Project description
pyABF provides a Python interface to 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.
Quickstart
Access 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 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)
plt.show()
Create Decorated 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="sweep %d"%(sweepNumber))
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
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