Reading different file formats

Neo is a Python package which provides support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon and Tdt.

The function reads data from any of the file formats supported by Neo and formats it for use in eFEL.

As an example, suppose we have an .abf file containing a single trace. Since eFEL requires information about the start and end times of the current injection stimulus, we provide these times as well as the filename:

import efel

data ="path/first_file.abf", stim_start=200, stim_end=700)

Since some file formats can contain multiple recording episodes (e.g. trials) and multiple signals per episode, the function returns traces in a list of lists, like this:

data : [Segment_1, Segment_2, ..., Segment_n]
         with Segment_1 = [Trace_1, Trace_2, ..., Trace_n]

Since our file contains only a single recording episode, our list of traces is:

traces = data[0]

which we pass to eFEL as follows:

features = efel.getFeatureValues(traces, ['AP_amplitude', 'voltage_base'])

Stimulus information within the file

Some file formats can store information about the current injection stimulus. In this second example, the file contains an Epoch object named “stimulation”, so we don’t need to explicitly specify stim_start and stim_end:

data2 ="path/second_file.h5")