I have two questions about working with the LFP data. Firstly in the tutorial on LFP analysis (here) they do not seem to be scaling the data at all and I heard the allen isntutute neuropixels data had a 0.195 byte/volt scale factor.
Secondly there seems to be some channels missing from a recordings for instance fro the first recording in probeE there are 73 channels from that probe in CA1, but in the lfp data only 18 exist.
Reproducible examples
# calling the metadata about the probes and channels from first recording and its LFP data
session = cache.get_session_data(sessions.index.values[0])
probe_id = session.probes[session.probes.description == 'probeE'].index.values[0]
lfp = session.get_lfp(probe_id)
But despite neuropixels probes have 364 channel (and one reference channel) there are only 73 lfp channels in the lfp data.
lfp.shape returns (12028993, 95). Furthermore if I check for the number of channels in a brain regions, for instance CA1, as listed by the structure annotations in the session object sotring the meta data there are far fewer lfp channels in the lpf object.
# check the number of channels from this probe in CA1
session.channels.structure_acronym[(session.channels.probe_id==probe_id)&(session.channels.structure_acronym=='CA1')]
# pulling those channles data will likewise give 73
ca1_chans =session.channels.probe_channel_number[(session.channels.probe_id==probeid)&(session.channels.structure_acronym=='CA1')]
# now we check for matching channel identifiers
ca1_idx = np.isin(lfp.channel.values, ca1_chans.index.values)
ca1_idx = lfp.channel.values[ca1_idx]
ca1_idx.shape
There are only 18 channels in the lfp for probeE which match based on channel identifier. Which is not surprising considering there are only 73 channels in that probe.
Have I simply chosen a bad probe? Please help me understand why there is missing LFP data.
Hi @AngCamp, these questions are likely better asked on the community forum https://community.brain-map.org/. If there ends up truly being an issue, open another github issue here.
I have two questions about working with the LFP data. Firstly in the tutorial on LFP analysis (here) they do not seem to be scaling the data at all and I heard the allen isntutute neuropixels data had a 0.195 byte/volt scale factor.
Secondly there seems to be some channels missing from a recordings for instance fro the first recording in probeE there are 73 channels from that probe in CA1, but in the lfp data only 18 exist.
Reproducible examples
But despite neuropixels probes have 364 channel (and one reference channel) there are only 73 lfp channels in the lfp data.
lfp.shape
returns (12028993, 95). Furthermore if I check for the number of channels in a brain regions, for instance CA1, as listed by the structure annotations in the session object sotring the meta data there are far fewer lfp channels in the lpf object.returns:
There are only 18 channels in the lfp for probeE which match based on channel identifier. Which is not surprising considering there are only 73 channels in that probe.
Have I simply chosen a bad probe? Please help me understand why there is missing LFP data.