Loading Spike Waveforms
Sample of spike waveforms extracted during spike sorting
Relevant Alf objects
_phy_spikes_subset
Loading
[2]:
from one.api import ONE
from brainbox.io.one import SpikeSortingLoader
from iblatlas.atlas import AllenAtlas
one = ONE()
ba = AllenAtlas()
pid = 'da8dfec1-d265-44e8-84ce-6ae9c109b8bd'
# Load in the spikesorting
sl = SpikeSortingLoader(pid=pid, one=one, atlas=ba)
spikes, clusters, channels = sl.load_spike_sorting()
clusters = sl.merge_clusters(spikes, clusters, channels)
# Load the spike waveforms
spike_wfs = one.load_object(sl.eid, '_phy_spikes_subset', collection=sl.collection)
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More details
Useful modules
COMING SOON
Exploring sample waveforms
Example 1: Finding the cluster ID for each sample waveform
[3]:
# Find the cluster id for each sample waveform
wf_clusterIDs = spikes['clusters'][spike_wfs['spikes']]
Example 2: Compute average waveform for cluster
[4]:
import numpy as np
# define cluster of interest
clustID = 2
# Find waveforms for this cluster
wf_idx = np.where(wf_clusterIDs == clustID)[0]
wfs = spike_wfs['waveforms'][wf_idx, :, :]
# Compute average waveform on channel with max signal (chn_index 0)
wf_avg_chn_max = np.mean(wfs[:, :, 0], axis=0)
Other relevant examples
COMING SOON