pyabf

pyABF: a pure-Python ABF file reader

pyABF provides a Python interface to electrophysiology files in the Axon Binary Format (ABF). pyABF supports Python 3 and does not use obscure libraries (just numpy and matplotlib). pyABF supports reading ABF1 and ABF2 files and can write ABF1 files.

.. class:: no-web

.. image:: http://swharden.com/pyabf/graphics/action-potentials-small.png
    :alt: pyABF electrophysiology data analysis with Python and Matplotlib
    :align: center

Quickstart

Install or upgrade pyABF:

.. code-block:: bash

pip install --upgrade pyabf

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Access ABF sweep data:

.. code-block:: python

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)

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Plot a sweep with Matplotlib:

.. code-block:: python

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

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.. image:: http://swharden.com/pyabf/graphics/pyabf-example-sweep.jpg
    :alt: pyABF Example
    :align: center

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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/

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.. image:: http://swharden.com/pyabf/graphics/pyabf-example-action-potentials.jpg
    :alt: pyABF Example
    :align: center

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