Handling probe information

In order to properly spike sort, you may need to load information related to the probe you are using.

SpikeInterface internally uses ProbeInterface to handle probes or probe groups for recordings.

Depending on the dataset, the Probe object may already be included or might need to be set manually.

Here’s how!

import numpy as np
import spikeinterface.extractors as se

First, let’s create a toy example:

recording, sorting_true = se.toy_example(duration=10, num_channels=32, seed=0, num_segments=2)
print(recording)

GroundTruthRecording (InjectTemplatesRecording): 32 channels - 30.0kHz - 2 segments
                      600,000 samples - 20.00s - float32 dtype - 73.24 MiB
Segments:
Samples:   300,000 | 300,000
Durations: 10.00s | 10.00s
Memory:    36.62 MiB | 36.62 MiB

This generator already contains a probe object that you can retrieve directly and plot:

probe = recording.get_probe()
print(probe)

from probeinterface.plotting import plot_probe

plot_probe(probe)

Probe - 32ch - 1shanks

(<matplotlib.collections.PolyCollection object at 0x73e4c5cd6230>, <matplotlib.collections.PolyCollection object at 0x73e4c5cd5300>)

You can also overwrite the probe. In this case you need to manually set the wiring (e.g. virtually connect each electrode to the recording device). Let’s use a probe from Cambridge Neurotech with 32 channels:

from probeinterface import get_probe

other_probe = get_probe(manufacturer="cambridgeneurotech", probe_name="ASSY-37-E-1")
print(other_probe)

other_probe.set_device_channel_indices(np.arange(32))
recording_2_shanks = recording.set_probe(other_probe, group_mode="by_shank")
plot_probe(recording_2_shanks.get_probe())

Probe - cambridgeneurotech - ASSY-37-E-1 - 32ch - 2shanks

(<matplotlib.collections.PolyCollection object at 0x73e4be9cf6d0>, <matplotlib.collections.PolyCollection object at 0x73e4be9cfc70>)

Now let’s check what we have loaded. The group_mode='by_shank' automatically sets the ‘group’ property depending on the shank id. We can use this information to split the recording into two sub-recordings. We can access this information either as a dict with outputs='dict' (default) or as a list of recordings with outputs='list'.

print(recording_2_shanks)
print(f'\nGroup Property: {recording_2_shanks.get_property("group")}\n')

# Here we split as a dict
sub_recording_dict = recording_2_shanks.split_by(property="group", outputs='dict')

# Then we can pull out the individual sub-recordings
sub_rec0 = sub_recording_dict[0]
sub_rec1 = sub_recording_dict[1]
print(sub_rec0, '\n')
print(sub_rec1)

GroundTruthRecording (InjectTemplatesRecording): 32 channels - 30.0kHz - 2 segments
                      600,000 samples - 20.00s - float32 dtype - 73.24 MiB
Segments:
Samples:   300,000 | 300,000
Durations: 10.00s | 10.00s
Memory:    36.62 MiB | 36.62 MiB

Group Property: [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1]

GroundTruthRecording (ChannelSliceRecording): 16 channels - 30.0kHz - 2 segments - 600,000 samples
                      20.00s - float32 dtype - 36.62 MiB
Segments:
Samples:   300,000 | 300,000
Durations: 10.00s | 10.00s
Memory:    18.31 MiB | 18.31 MiB

GroundTruthRecording (ChannelSliceRecording): 16 channels - 30.0kHz - 2 segments - 600,000 samples
                      20.00s - float32 dtype - 36.62 MiB
Segments:
Samples:   300,000 | 300,000
Durations: 10.00s | 10.00s
Memory:    18.31 MiB | 18.31 MiB

Note that some formats (MEArec, SpikeGLX) automatically handle the probe geometry. For almost all other formats the probe and the wiring have to be set manually using the probeinterface library.