Skip to main content

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

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pyabf-2.3.6.tar.gz (44.3 kB view hashes)

Uploaded source

Built Distribution

pyabf-2.3.6-py3-none-any.whl (53.2 kB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page